When I turn the key off on my 2001 4Runner only the engine will shut off. All of the electronics stay on. I have to take the negative off the battery in order to turn everything off. Any solutions?

sticking relay contacts in the PCM power relay , maybe . It's located in the central junction box . That is the inside the vehicle fuse box. That relay supply's power to the engine computer , ignition system , fuel etc.... If the contacts are stuck closed or sticking the engine would keep running with key off .

Check connection of battery terminals to it's related cables. Try using one of the jumper cables to connect negative of battery to chassis.if still fail, try connecting to engine block. If fail, try recharging/replacing battery. Lights may stay bright but battery may mot have enough amperage to turn starter motor.

Did you check the battery an connections , does the engine spin over when turning the key to start ? Light's work on the dash with key on . Is the SECURITY light on or flashing ? If the engine does spin with the key in the start position , is there spark ? pull a coil an see if there is spark ! If no spark , could have a crankshaft position sensor problem ! Do a fuel pressure test . etc... This is a very complex electronically controlled vehicle , you should consider taking it to the dealer !

Maybe this will help:
From the owners manual:

SENTRY KEY IMMOBILIZER - IF EQUIPPED
With this system, an electronically coded ignition key
sends a signal to the vehicle electronics. If the electronics
recognizes the signal, the vehicle will start and continue
to run. If the system does not recognize the signal, the
vehicle will start and run for 2 seconds, then shut off.
After six unsuccessful attempts at starting, the system
will shut down until the correct key is used.

That's exactly what happened when I cut a new key and tried to start the truck without programming the key. So it looks like your truck is not recognizing the key.
If you have another key, try that one.

Or, try and disconnect the battery for a while, that clears up a lot of electrical problems.

GL,
Td

sounds like antitheft system is acting up..needs reprogramed maybe..pull the negative cable with the key on....kills everything..then shut the key off..reconnect the negative.. turn the key to run position for a few seconds(resets all factory presets) see if it will start..

Fan will run for a certain period of time after shutting down motor of vehicle. This is normal. Your engine is still hot when you turn the key off. There are sensors that tell the computer when the engine is cool enough for the fans to shut off.

Did you do it like this? Voltmeter: black lead on negative battery terminal, positive lead on one of terminals on coil side- turn key to on, and see if there is voltage for about 2 seconds. If yes, check negative terminal of relay's coil side. If no voltage, move positive lead to other terminal for coil side. Turn key to on, and see if you have voltage for about 2 seconds. If yes, test negative side of relay's coil for good ground. If no signal at either terminal, the signal may be lost from the pcm.

When you turn the key to on, this will prime the fuel system-pump will turn on for only 2 seconds with key in on, and then if no crank signal, pump will turn off (the relay will not stay energized, so no power will go to pump). But when the engine is cranking over, the relay is energized, the coil side will stay powered as long as engine is cranking. After the engine is running, usually an oil pressure switch is tied into the fuel pump circuit, so the relay is no longer needed to put power to the pump. The pump will always be running when engine is cranking, and when engine is running, but the relay no longer is needed when engine is running. See?

You are dealing with 2 possible problem. The ignition switch,or the alarm, If you have a alarm problem the vehicle will crank then in 2 seconds shut down,this is because the key is recognized,now if this is the problem roll down a window and disconnect the negative battery terminal,put the key in the ignition but in the off position.After 5 minutes reconnect the battery and turn the ignition on but dont crank the engine leave for 1 minute. Then see if that resolved the issue.Now if its an ignition switch problem crank the engine and slowly let it go.try to keep the key in the position where it stays running. By the way there is a campaign of a recall dealing with a TIPM software update Re-configure ,anti-theft system. Customer satisfaction notice G42. You will have to see the dealer for this campaign.

Replace the starter.

Removal & Installation

1.5L & 1.6L (VIN 5) Engines

1. Before servicing the vehicle, refer to the Precautions Section.
2. Disconnect the negative battery cable.
3. Remove the 4 upper intake manifold stay bracket bolts.
4. Disconnect the starter electrical connections.
5. Remove the upper starter bolts.
6. Remove the lower starter mounting bolt(s) and the starter.
   
   

   Fig. Starter mounting-1.5L and 1.6L engines
   

To install:

1. Install the starter.
2. Install the lower starter bolt and tighten to 27-38 ft. lbs. (37-52 Nm).
3. Connect the starter electrical connections.
4. Install the intake manifold support bracket and finger-tighten the 3 mounting bolts. Tighten the lower bolt to 27-38 ft. lbs. (37-52 Nm).
5. Install the 4 upper intake manifold stay bracket bolts and tighten to 27-38 ft. lbs. (37-52 Nm).
6. Install the upper starter bolts and tighten to 27-38 ft. lbs. (37-52 Nm).
7. Connect the negative battery cable.

1.6L (VIN 3) Engine

1. Before servicing the vehicle, refer to the Precautions Section.
2. Remove or disconnect the following:
   
   Negative battery cable Air intake assembly Shift cable and bracket Starter electrical connections Starter
   

To install:

1. Install or connect the following:
   
   Starter Starter electrical connections Shift cable Air intake assembly Negative battery cable
   

pull out negative terminal battery located under rear right seat.wait for 5 min n then install again the lead negative terminal.insert the key to ignition cylinder.turn the key on off three times.now start the engine.make sure u use recommended fuel grade.