I had the same question with my '00 cherokee.
I posted a question in this forum and did a search...basically I got different answers.
From what I read, electric cooling fan on OBDII cherokees...98-01 is controlled by the ECM. The ECM will turn on/off the fan based on AC system requests and temperature readings.
Most posts and articles I've read stated that the fan should come on when the AC is turned on. I think this is true on vehicles that just have electric cooling fan or fans. Since the 98-01 (and mybe others) cherokees have a mechanical fan for primary cooling, I'm not sure this is true. The electric fan may or may not come on when the AC is turned on.
I have yet to see my turn on...but its been relatively cool lately where I live. On my cherokee, I've verified that the fan and fan relay is good. The ECM is just not sending a signal (ground the relay) to turn it on. Now my ECM might be bad...but since it is not running hot (I think), I'll wait for warming weather to do further testing.
from
http://findarticles.com/p/articles/mi_m3102/is_10_123/ai_n6358902
"The system is simple and direct, with the PCM controlling the A/C clutch and the secondary engine cooling fan through a pair of relays. The 4.0L package has a belt driven fan as well as an electric cooling fan to assist in case the A/C head pressure goes too high or the engine gets too hot....
The secondary fan only runs when the PCM determines it is needed, either in response to engine temperature or a ground from the A/C high pressure switch. As Ed's Jeep heated up and the A/C head pressure climbed, we watched the high-pressure switch open Circuit C90, giving us 12 volts once again, and within a second or so, the PCM triggered the cooling fan relay to energize the secondary fan."