The filter is located in the fuel tank. You do not need to drop the gas tank from the car; however, this is a major job, so be very patient (the first time you do it could take 3-4 hours). Here's what you'll need to do if you really need to replace the fuel filter:
1. First, make certain that you've got a bad filter. These filters typically last for many years, and are designed to last a very long time. Perform an engine diagnostics test using a Toyota hand tester into the DLC3 socket (an outlet to plug the tester into, that's located under the steering wheel). This is just to see if your fuel pump isn't the culprit.
2. Now to remove the fuel pump to get to the fuel filter (if you've determined it's most likely the fuel filter and not the pump). Remove the rear seat cushion, then remove the floor service hole cover. Disconnect the battery cable from the battery. Sparks, flames, and lit cigarettes wouldn't exactly be the best things to be exposed to at this time.
3. Disconnect the fuel pump and the sender gauge connection.
4. Disconnect the fuel tube.
5. Wash away the mud, dust and the likes on the fuel suction plate with water.
6. Pull off the tube joint clip form the fuel suction plate.
7. Disconnect the fuel tube from the fuel pump assembly.
8. Affix the tape in order to protect the port portion from the dust and elements. Blue painters tape would be best, as its not loaded with so much adhesive that might cause contamination.
9. Prevent the disconnected fuel tube from damaging and mixing foreign objects by covering them with a vinyl bag.
10. Remove the fuel pump from the gas tank.
10.1 Remove the 8 bolts and fuel tank vent tube set plate.
11. Pull fuel pump out of the tank
11.1 Caution - Do not damage the fuel pump filter.
11.2 Caution - Be careful not to bend or damage the arm of the sender gauge, remove with care. Damage to either of these items will be expensive to replace, and its easy to damage these items.
12. Remove the gasket from the pump assembly.
13. With the fuel pump removed: Remove the # 2 fuel suction support.
13.1 Using a small screwdriver, remove the No. 2 fuel suction support.
13.2 Remove the rubber cushion and fuel pressure regulator.
13.3 Remove the O-ring from the pressure regulator.
14. Remove the # 1 fuel suction support.
14.1 Disconnect the fuel sender gauge connector.
14.2 Using a small screwdriver, remove the No. 1 fuel suction support. Caution - Do not damage the fuel suction support and fuel suction plate.
14.3 Disconnect the fuel pump harness from the fuel pump.
14.4 Remove the O-ring from the No. 1 fuel suction support.
15. Remove the vapor pressure sensor. Pull off the joint clip and remove the vapor pressure sensor from No. 1 fuel suction support.
16. Remove the fuel filter
16.1 Remove the fuel pump from the fuel filter.
16.2 Remove the O-ring from the fuel pump.
Go get yourself a case of beer and enjoy it. You'll need the rest when you attempt to put everything back together.
It is very helpful to use the pictures from the shop manual for this job. Also in my opinion you should never replace ONLY the pump or filter, you should replace them together. If you go to all the trouble of pulling the assembly out, it just makes sense to change them both at the same time as it will not add any time to the job and the cost is minimal. You can find both the pump and the filter for about $20 each including shipping, on eBay (check seller feedback to make sure they have favorable reviews).
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