2004 Toyota Highlander 3.3 auto.
Friend wanted me to look at his car and it’s over my head, so I’m going to give it back without fixing it. Unless maybe someone here can help.
Engine cooling fan (not the fan controlled by A C) is constantly on with key off and engine cold. When the battery went dead they had a mechanic change out the battery and alternator. The new alternator looks like a universal unit and not vehicle specific. When their battery went dead again, they replaced it and bring it to me. When I got it the fan connector was unplugged. When I plugged it in, it would constantly run. I swapped relays, no help there. Compared ohms on the two relays I swapped and they are similar. Battery tested great. Alternator voltage was 13.1 volts. Took it for a test drive and it drove a little funny for a minute until the computer found it’s bearings then ran fine. When I returned from the test drive, I checked charging voltage at 14.x volts.
And fan turned off when I turned off the key. Battery light is still on in dash. When I unplug connector for alternator signal at alternator everything goes to battery voltage. I checked all fuses related to charging system. #9 Alt-S charging system fuse was blown 7.5 amp. When I put another fuse in it activated the fan relay. It idled a little slow (maybe) and did not have charging voltage. I removed the fuse and charging voltage slowly went to 14.x volts and idle went up. Then I removed fan relay and everything seemed fine. Had charge and alternator light is off. Then with fan relay still out the alternator fuse blew and dash light came back on and still had 14.x volts. It seems to me that there is a short somewhere between the fan and the alternator fuse. Does anyone have an idea of some simple solution based on your experience? Otherwise I’m going to send this back, and he can pay for a professional.
The fan is killing the battery. This isn’t a charging system problem. Find a good mechanic to chase this down. I don’t understand why the prior one replaced the alternator.
The fan is killing the battery. But when I remove the fan relay the alternator fuse still blows. That is the root problem. It will probably end up at a professional, but just looking for ideas in the meantime.
That’s a tough diagnostic problem you got there. The way the cooling fan works on my older Corolla, a coolant temp switch (which is screwed into the coolant jacket) opens when the coolant gets above a certain temperature, and that causes the cooling fan relay to close its contacts which powers the fan. That temperature switch goes bad once in a while and the way I tell its the switch and not the fan motor or the relay is I disconnect the switch, which immediately causes the fan to turn on. All that is probably of no value to you b/c on a 2004 the fan is probably turned on and off by the powertrain computer, based on a formula derived from the same coolant temperature sensor it uses to set the air/fuel mixture.
hmm … so what else? Well, I had a problem with the alternator not charging the battery one time on the same Corolla. That turned out to be the main wiring harness developed an open circuit between the alternator and the battery. Battery acid leaked from the battery, down the cable, into the middle of that harness. Eventually it reached a solder joint, and promptly ate through it. It was quite a difficult job cutting that harness apart, figuring out where the break was, and re-soldering that solder joint I must say. I had to buy a heavy duty soldering iron just for that job in fact. Sorry, but can’t be of much more help than that. It might give you some clues anyway.
Thank you. I did consider the coolant temp sensor, and the only thing that steered me away from it is that my scanner matched the dash temp gage. I did return the vehicle this afternoon. I was informed that the fuse problem and battery drain problem didn’t start until the new alternator was installed. And I still don’t know why they had the battery and alternator replaced. I’m getting different accounts of things so it was getting harder. They are going to take it to a shop. If it were my car I’d get a wiring diagram and see how the fuse corralates with the fan and go from there. If I couldn’t figure it out by doing that, I’d probably shotgun a 220 dollar alternator into it and start cussing because it still don’t work. Then I’d look for hours and find out it was something simple. But it’s out of my hands now. 
Call your local Toyota dealer parts department and see if your neighbors year Highlander uses a fan control module.
Faulty alternators can definitely cause battery drain problems. Bad diode for example will allow the battery to drain through the alternator circuitry, overnight. That might not show up in an alternator functional test, but would in a parasitic drain test. Wouldn’t normally be enough to blow a fuse though.
Just for closure: they took it to their mechanic and he found a short in the distribution center. 1 hour labor, Happy ending.