R6 fans not running

2009 R6 fans don't run even at the high temp warning point.

- fuse checked
- hooked the fans up to the battery directly and they both work
- thermostat causes the radiator to cycle the fluid (thermostat should be fine?)

I'm guessing it's probably the fan relay switch? I have no idea where it's located but guessing if there's no break in the harness from the switch relay to the fan fuse box location, it must be the relay itself.

Any other suggestions? Any help would be greatly appreciated.

did it stop working or never seemed to work? Might need to go beyond the warning point to activate.

Check the thermal switch. They are usually on the radiator. That's prob not thorwing the fan on. Try by passing the sensor - to see if the fan will come on (paper clip)

Let me know if you need help - glad to helP!

Thanks for the response.

Riceburner -- yes they were previously working.

frekeyguy -- good idea. I'll give that a shot and see how it goes.

sys49152 said:

2009 R6 fans don't run even at the high temp warning point.


- fuse checked
- hooked the fans up to the battery directly and they both work
- thermostat causes the radiator to cycle the fluid (thermostat should be fine?)


I'm guessing it's probably the fan relay switch? I have no idea where it's located but guessing if there's no break in the harness from the switch relay to the fan fuse box location, it must be the relay itself.


Any other suggestions? Any help would be greatly appreciated.

Click to expand...

Does the coolant temperature display on the dash read the correct coolant temperature? Your fans are supposed to come on when the coolant temperature display on the dash reaches 102c (216f).

Your fans are completely controlled by the ECU. Try testing them in diagnostic mode and see if the relay is functioning and the ECU control signal is working properly:

Your service manual: http://ecuflashking.com/r6/manuals/2008-2011 Yamaha R6/2008 Yamaha R6 Serivce Manual.pdf

Diag mode:

1. Set the kill switch to STOP.

2. Hold down the select and reset buttons and turn the key to ON while still holding them down.

3. After you continue to hold the select and reset buttons for about 10 seconds the dash should say "DIAG". Release the select and reset buttons and then hold them again until the dash says D01.

4. If you twist the throttle you should see the D01 number go up and down, D01 is your throttle position sensor test.

5. You can press the select or reset buttons to cycle through all the tests. D06 is the test for the coolant temperature sensor (just reads out the currently sensed coolant temperature) and D51 is the radiator fan motor relay test. It will actuate the radiator fan motor relay five times at one second intervals (ON 2 seconds, OFF 3 seconds) and also illuminates the engine trouble warning light. If the D51 test doesn't produce any reaction from the motorcycle try it again with the kill switch set to RUN or cycling the kill switch while the D51 test is selected. Use extreme caution using diag mode with the kill switch in the RUN position, if you hear your fuel pump running for more than 5 seconds turn the kill switch back to stop or if that doesn't stop the fuel pump turn the key to off.

Troubleshooting steps start at page 354 of the service manual (8-31) with the radiator fan motor relay inspection/testing procedures in the lower left of page 413 (8-90).

I've seen this problem twice before, when people either connected their main battery backwards, or were boosting it and connected the booster cables backwards. It damaged the fan relay controller inside the ECU. Wiring up a manual fan switch fixed the problem (you just turn it on to cool the bike down) or you can replace the ECU. If your bike is a canadian bike (has red blinkie light in tach gauge) then purchase a replacement ECU from the USA (approx $150, any 2008 to 2015 ECU will work) and I can modify it to work on your bike. If your bike is a USA bike (no red blinkie light in tach gauge) then any 08-15 USA ecu will work in it without modification. To buy a Canadian ECU from yamaha would cost $2800 and you'd have to replace your ignition, keys, gas cap and trunk lock, that's why you go the USA ECU route.

I'm just in Whitby if you want to bring your ECU by (or if you think it's safe enough to ride your bike down) I can plug it into my laptop and run the fan control test as well as reset the eeprom values for the fan turn on and off temps (and I could temporarily set them way lower so it doesn't have to get to 102c before it's supposed to turn your fans on). I also have a spare ECU we could try in your bike (or you could borrow to help in your troubleshooting). Everything I've mentioned above (with the exception of converting a USA ecu to work on a canadian bike) would be free of charge. You can text 289-600-9937 if you need to get a hold of me (calls don't work).

Good luck!

mine sometimes does not go on till 110* c and some times it just starts on 99 and i am guessing it depends on the type of coolant u have in your bike.

ps: i ride an 06 and use prestone coolant

johnscruiser said:

Does the coolant temperature display on the dash read the correct coolant temperature? Your fans are supposed to come on when the coolant temperature display on the dash reaches 102c (216f).
....
Good luck!

Click to expand...

Thanks for the detailed response and suggestion. I didn't even think of trying the ecu diagnostics. I'm pulling the bike out of storage this weekend, so I'll give this a try. I had my ecu flashed a few years ago (you might remember, as it didn't go as smoothly as we hoped.. I think I was the first or second to give it a shot), but if need be, I'll give you a call.

blessedlife said:

mine sometimes does not go on till 110* c and some times it just starts on 99 and i am guessing it depends on the type of coolant u have in your bike.

ps: i ride an 06 and use prestone coolant

Click to expand...

It's hit well over a 110 without coming on. Enough to have the warning light come on. I usually run water + water wetter or mocool.

sys49152 said:

Thanks for the detailed response and suggestion. I didn't even think of trying the ecu diagnostics. I'm pulling the bike out of storage this weekend, so I'll give this a try. I had my ecu flashed a few years ago (you might remember, as it didn't go as smoothly as we hoped.. I think I was the first or second to give it a shot), but if need be, I'll give you a call.

Click to expand...

Sounds good. Text, not call

They came out with some awesome new features vs. the early flashes like speedo calibration for different sprocket sizes (no speedo healer required), disabling of the AIS/smog pump (for less pop and backfire and great for running autotune), re-enabling of the immobilizer if it was disabled with the early flash (fixes er-4 error when trying to go into diag mode), fixed the high idle or varying idle (especially after you've been riding around for a bit), etc. I can update your flash for ya for no charge.

So, if your bike is canadian (has red blinkie light) and you're on the early version of the flash, you won't be able to use diag mode unless a) I re-flash your ECU to enable the immobilizer (free, only works if you've got the original red or black transponder keys) or b) you disconnect your immobilizer (it's under the front of the airbox, not the easiest place to get to. Great time to install smog plates and change your spark plugs while you're in there that deep). You can leave the immobilizer disconnected and the bike will still work perfectly, just won't have a red blinkie light on the dash.

Immobilizer connection: