Where is flasher located 1999 ford explorer

There is no flasher relay , all done electronically by the smart junction box (computer )
The smart junction box (SJB) monitors the multifunction switch position by sending multiple voltage reference signals to the multifunction switch. When the multifunction switch is in the LH or RH TURN positions, or the hazard lamp switch is engaged, that input signal is routed to ground.
When the SJB receives an input from the multifunction switch indicating a request for a turn signal or hazard lamps, the SJB then supplies voltage to the appropriate turn lamps.

Your best bet would be to take it to a qualified repair shop or dealer .
Do you know what DTC'S are ?
Smart Junction Box (SJB) Diagnostic Trouble Code (DTC) Chart DTC Description Action B1499 Lamp Turn Signal Left Circuit Failure Go To Pinpoint Test M . B1502 Lamp Turn Signal Left Circuit Short to Ground Go To Pinpoint Test M . B1503 Lamp Turn Signal Right Circuit Failure Go To Pinpoint Test M . B1506 Lamp Turn Signal Right Circuit Short to Ground Go To Pinpoint Test M . B2048 Left Rear Turn Lamp Circuit Short to Ground For Mountaineer, Go To Pinpoint Test M .
For Explorer or Explorer Sport Trac, REFER to Stoplamps in this section. B2049 Left Rear Turn Lamp Circuit Open For Mountaineer, Go To Pinpoint Test M .
For Explorer or Explorer Sport Trac, REFER to Stoplamps in this section. B2050 Right Rear Turn Lamp Circuit Short to Ground For Mountaineer, Go To Pinpoint Test M .
For Explorer or Explorer Sport Trac, REFER to Stoplamps in this section. B2051 Right Rear Turn Lamp Circuit Open For Mountaineer, Go To Pinpoint Test M .
For Explorer or Explorer Sport Trac, REFER to Stoplamps in this section. B2071 Hazard Switch Signal Short to Ground If the hazard lamps are inoperative, Go To Pinpoint Test N .
If the hazard lamps are always on, Go To Pinpoint Test O . B2281 Right Turn Switch Short to Ground Go To Pinpoint Test L . B2282 Left Turn Switch Short to Ground Go To Pinpoint Test L . All other DTCs - REFER to Section 419-10 .

You will need the factory wiring diagrams. We do not have them due to copyrighting. You can buy the factory wiring booklet HERE, a must have for doing your own electrical trouble shooting and worth every penny.

For 1999 Ford Truck Explorer 4WD 4.0L EFI SOHC 6cyl check the Flasher; this is located in front seating area, driver side, behind dash, mounted on steering column .

Hope this helps (remember to rate and comment this answer).

look under the dash to the right of the steering wheel. both the turn signal and hazard light relay should be there.

Try changing the fuse....even if it looks fine. Then, the flasher....and last, the turn signal cam.....which is part of the turn signal arm assembly (you have to pull the steering wheel off).

The 2 fuses are no 10 (7.5amp) and no 21(15amp) in the interior fuse panel.The flasher is located on the base of steering column under dash. See this this pic find connector c214 on bottom 3rd from right.
http://i253.photobucket.com/albums/hh43/chuck943/EXN15113.gif

It is behind center of instrument cluster just above the accel pedal in the blower/flasher relay block,it is actually a relay on this vehicle.

You find the flasher on the steering column. You have to remove the cover located between the steering wheel and instrument panel. There you find the flasher.
Before replacing the flasher check the wirings to the flasher.

In the auxilary box under dash near ashtray to the right of accel pedal.