11 Common Problems With the Yamaha R6 (Solution Guide)

The R6 is one of the most advanced supersport machines ever built and is a perennial favorite among sportbike fans.

Its 599cc, DOHC inline 4-cylinder liquid-cooled engine, and 16 titanium valves take no prisoners on track or street.

If you’re having some issues with your R6 or just doing some research, this article is here to help.

1. Yamaha R6 Won’t Start

If your Yamaha R6 makes a clicking noise but won’t turn over. If nothing happens, it may be a safety feature that needs to be reset.

The R6’s engine is regarded as top-notch in the sportbike community… and then some.

Still, all motorized mechanisms are prone to fail at some point.

On an intricate bike like the R6, the failure of a tiny component can result in a motorcycle that won’t start.

Dead Battery

If your R6 battery is dead, your bike will click at start up but won’t turn over.

  • The battery is the powerful force of all your R6’s electrical components, including your bike’s ignition, starter, and fuel injection systems.
  • In some cases, the battery fails to power the starter because of a low charge. The click sound your R6 makes is because the battery has enough juice to zap the starter but not enough to move the coil to start.
  • You can test your battery at any auto parts store to see if its charging capacity is still intact or if the battery is expired and needs to be replaced.
  • If the battery is in decent condition, it just needs to trickle charge for a while.
  • In other cases, if the battery is expired, you’ll need to replace it.

Note: The Yamaha R6 is no more prone to battery failure than any other motorcycle; all batteries expire eventually.

Faulty Starter

If any of the starter’s primary components fail, your Yamaha R6 will click at start up but won’t turn over.

In order to explain this more thoroughly, let’s examine the three main components and functions of a motorcycle starter.

  1. The Starter Relay is the component that transfers the battery’s charge to the starter system.
  2. The solenoid is the stater’s electromagnet generator that activates your R6’s starter motor once charged by the relay.
  3.  Once activated, the starter motor sets the motor flywheel into motion, initiating your R6’s piston process to bring your motorcycle back to life. 

If your Yamhaa’s battery is dead, the starter will click at start up, as the residual charge is enough to juice the relay but not to magnetize the starter motor.

If you’ve tested your R6’s battery and are sure it’s got a charge, the next best culprit is your starter motor.

The failures are similar in nature and thus are often confused.

The difference is that the clicking sound in this scenario is the starter gears failing to turn your flywheel over; it’s caused by failed magnetization, either from a lousy magnet or a bad starter motor.

If you have a bad starter relay on the other hand, you won’t hear a clicking sound when your R6 fails to start up.

This is because the starter magnet can’t get the juice it needs to click if your relay isn’t working properly. 

Seized Engine

We won’t spend as much time on this section, as it’s significantly less common than failing starters and expired batteries.

Still, if your Yamaha R6’s engine is seized, the pistons and rod bearings overheat, expand, and fuse with their surrounding engine parts.

  • Eventually, the overheating seizes the flywheel. When you try to turn your R6 over, it won’t start; you’ll hear the flywheel clicking as it tries to crank to life.
  • Engine seizures on Yamaha R6s are often due to hardcore track riding, especially on models affected by aftermarket customization.
  • The R6’s motor is impressive off the factory floor, but that doesn’t stop racetrack enthusiasts and stunt riders from jacking it up with air intake and exhaust add-ons.

If not tuned and maintained correctly, these parts fail to integrate with the stock engineering and overheat the R6 to the point of failing to start.

ECU Throws Code/Needs Resetting

Your Yamaha R6 won’t start if you drop your bike, and its safety switch is activated; it will not start until the motorcycle is reset.

Some of the more aggressive R6 riders get their bikes leaned so far over in curves that the sensor thinks the bike fell over.

  • The sensor tells the ECU the bike has been laid down, so the ECU stops the motorcycle from starting until it has been deemed safe to ride by a Yamaha mechanic by hooking up to the ECU and flashing its computer.
  • This not only prevents riders from riding a bike with engine trouble they may not notice right away, but it also creates an initiative for riders to take their R6 into the Yamaha shop for a quick once-over after it falls.
  • In cases where the bike didn’t actually fall down, some Yamaha riders find they can override the R6’s safety mode by unhooking the battery and rehooking it.
  • Other riders claim they’ve tried a “field flash” by unhooking the battery, and it didn’t work.

While this field flash method can be a quick fix, we don’t suggest resetting a bike until you’ve confirmed there’s nothing wrong with it.

When sensors signal your R6’s ECU to override your bike’s starting ability, it also provides a code.

The code must be inspected and cleared for the bike to start.

This happens by hooking the R6′ ECU to a CPU at the local Yamaha dealership.

You can find online digital versions of the Yamaha R6’s Service Manual fr your particular year and model.

Distinguished from the owner’s manual that came with it, the service manual is written for the Yamaha service technicians and contains detailed explanations of all codes.

Here’s an example of a Code Description from the Service Manual of a 2008 Yamaha R6:

Fault code No.: 60

Symptom: Throttle servo motor: open or short circuit detected. Defective throttle servo motor. Malfunction in ECU (servo motor driving system).

Probable cause of malfunction:

  • Open or short circuit in wire harness.
  • Defective throttle servo motor (potentiometer circuit).
  • Stuck throttle servo motor (mechanism).
  • Stuck throttle servo motor (motor).
  • Malfunction in ECU.

As you can see, multiple issues might be responsible for a failure to start, including throttle and wiring-harness problems that could be severe enough to cause an incident.

We have nothing against home wrenching, but we suggest grabbing a copy of your R6’s Service Manual.

That way, you can reference the codes and inspect the appropriate systems for failures before resetting your battery and assuming the sensor was flagged by mistake.

2. Yamaha R6 Won’t Stay Running

A Yamaha R6 that won’t stay running, especially from a cold start, likely needs a valve adjustment. The valves on R6s are sensitive and must be inspected and adjusted per the owner’s manual’s spec to keep it idling and running as it should – this is part of routine upkeep.

The pre-2008 R6 models had particularly fussy valves on them that would stretch after a mere 5,500 miles of road roasting.

That said, from 2008 onwards, the R6 may have had much more stable valves.

Valve inspection is a routine part of maintenance on any R6.

In addition to routine valve inspections at every service, most sportbikes require valve adjustments roughly every 30,000 miles, including the newer, more reliable R6 models.

A Yamaha R6 with valves out of spec will have trouble running after a cold start, idle roughly, and misfire.

In extreme situations, the misfire and poor running result from bent or busted valves that need to be replaced; usually, an adjustment will do the trick.

Related: How Long Does a Yamaha R6 Last?

3. Yamaha R6 Won’t Crank

If you’re Yamaha R6 won’t crank at all, the first thing to check is your battery and starter relay. If both of those components are functioning, check the bike is in neutral and that its side stand sensor isn’t damaged or dysfunctional.

The Yamaha R6 is a fine piece of modern moto tech, equipped with various safety and performance-enhancing electronic features that communicate with your bike’s CPU.

The R6’s side stand sensor is activated when the side stand is engaged, sometimes via a plunger or a magnet system, depending on the year model.

Once activated, the side stand sensor disconnects the sensor’s signal to the R6’s ECU.

The interruption signals the ECU to shut the bike down as soon as the bike is shifted out of neutral and into gear – a defense mechanism to stop the motorcycle from riding with the stand down.

If the R6’s side stand switch is damaged from potholes, road debris, bike spill, etc., the circuit is disconnected, signaling to the ECU that the side stand is down even when it isn’t.

This triggers the ECU to stop your Yamaha R6 from cranking.

If the side stand switch is damaged, or if your R6 is in gear with the kickstand down, the bike won’t even try to crank.

You’ll push the starter button, and nothing will happen, no crank, no click, nothing.

4. Yamaha R6 Won’t Start When Hot

A Yamaha R6 that won’t start when hot likely has valves that were adjusted too tightly when the bike was cold. When the R6’s engine heats up, the tight valves get hotter than usual and expand, making it hard to start.

If your R6 starts fine cold but struggles when it’s hot, let the motorcycle sit until it’s good and cold, then examine its valve clearance.

If the valve clearance is too tight, you’ll know what your problem is.

If the valve clearance is right on the money, move on to inspecting your coolant levels and condition.

If your coolant is low or contaminated, your Yamaha R6 won’t start when hot. 

5. Yamaha R6 Won’t Go Into Neutral.

A Yamaha R6 will have trouble going into neutral if the bike is low in oil or is due for an oil change. Shifting is more effortless on a wet clutch like the Yamaha R6 when the oil is fresh and at spec levels.

If you inspect your R6’s oil and find that it’s great and filled to spec, but the bike still won’t go into neutral, try rolling the motorcycle forwards and backward a few times.

Sometimes the force of the pinched clutch just holds the bike in gear.

Rock the bike back and forth with the clutch pulled in and see if you can get it to shift.

If that doesn’t work:  

  1. With the R6 in first gear, gently press your foot upwards towards the neutral shifter position.
  2. Pull the clutch in and start the bike.
  3. Maintaining that light pressure on the foot control, hit the throttle a few times. Keep the clutch lever all the way pulled in and the clutch totally disengaged, so the bike doesn’t lurch forward while you brap the throttle.
  4. With some gentle upward pressure, the shifter foot control should leap up to neutral after a few throttle revs.

6. Yamaha R6 Won’t Rev Up

A Yamaha R6 that turns over but won’t rev up when you twist the throttle likely has a faulty throttle system, either with the position sensor or the control wire. If the throttle system is intact, there’s probably an issue with the air intake.

Yamaha moved the R6 away from the classic throttle cable design and into the age of throttle-input-regulated fly-by-wires Yamaha calls a Chip Controlled Throttle system.

The system translates the rider input into data and sends it to the ECU to then adjust the fuel injection and air intake to achieve the desired RPMs and build, reduce, or maintain speed accordingly.

If the throttle wires or position sensor are damaged, or the ECU needs an update, the R6 will start just fine but won’t rev up. 

7. Yamaha R6 Won’t Go Into Gear

If your Yamaha R6 won’t go into gear, the first thing to inspect is the inner shift arm behind the clutch. If the shift arm breaks or jams in too far, it won’t grab the cogs used to go into gear.

The first thing to inspect with shifting trouble is your oil level and condition.

Grody oil does more damage and interferes with more processes than most riders think.

Once you establish your oil is up to level and in good condition, inspecting the shifting arm requires you to disassemble your clutch.

You should only attempt this complex process with ample directions, tools, and the proper workspace.

If you’re inexperienced as a home mechanic, but your Yamaha R6 won’t get in gear, we suggest taking your R6 to Yamaha techs for clutch and shifter arm inspections and adjustments.

Related: Yamaha R6: 16 Most Common Questions (Answered)

8. Yamaha R6 Not Idling

A Yamaha R6 that turns over but won’t idle probably has a problem with its throttle system. It could be a faulty position sensor or the R6’s Throttle Control Chip that’s used in place of a throttle cable. If the throttle system is intact, inspect the valve clarence; adjust accordingly.

Yamaha stocked the R6 with throttle-input-regulated fly-by-wires Yamaha calls a Chip Controlled Throttle system.

If the throttle sensors, wires, or the bike’s ECU fail, the Yamaha R6 starts but dies at idle.

9.Yamaha R6 Keeps Turning Off

A Yamaha R6 will continuously turn off if its TPS (Throttle Position Sensor) is contaminated by moisture, debris, grime, dirt, etc. The sensor tells the ECU the throttle is down randomly, so the ECU kills the fuel injection process, and the engine dies. 

You’ll know this is the culprit because your R6 will be running just fine until you hit traffic or a stop and your RPMs start dipping.

Once the RPMs drop, the sensor thinks the throttle is somewhere it’s not, killing the fuel supply and thus your Yamaha’s ignition.

You can fix the problem by uninstalling the Throttle Position Sensor and cleaning it free of dirt and grime.

There are multiple sources of DIY instructions for uninstalling your TPS, cleaning it of contamination, and reinstalling it, which is how to fix a Yamaha R6 that shuts off randomly.

10. Yamaha R6 Battery Keeps Dying

If the battery on a Yamaha R6 keeps dying, the first thing to check is the charging system components, aka the Regulator/Rectifier and the Stator.

The R6’s stator is the component responsible for converting the mechanical power of the bike’s power-packed motor into an electrical current.

The Regulator/Rectifier rectifies the current, so the battery can use it to recharge while you’re riding.

It also regulates the charge, so the battery doesn’t explode.

A failing Regulator/Rectifier or Stator is the leading two causes for a battery that keeps dying and won’t charge on a Yamaha R6.

11. Yamaha R6 not getting fuel

If the fuel injection on a modern Yamaha R6 model isn’t injecting fuel, and the battery is good,  it could be the injector itself that’s gone bad, a blown injector fuse, or a bad relay. The usual culprits on an older, carburated R6 are float needle issues, bad carb jets, or clogged fuel lines. 

Related: 9 Most Common Problems With Yamaha YZF R125 (Explained)