The meanings are really the same. Both are asking about a future expectation. 
 
"When is he coming to fix it?" This is more natural and "informal" sounding. Perhaps use this one, when asking a family member who already has the information.

"I have to run to the bank, honey, make sure you're around for the repair guy coming to fix the air conditioning."

"Ok. When is he coming to fix it?"

"When will he come to fix it?" is more formal sounding. Perhaps this should be used when asking the company "he" works for when he will come.

"I'm sorry for the delay Mr. Park, our serviceman is running a little behind for your appointment."

"So when will he come to fix it?"

(You could also say "When will he be here?" or "What time can I expect him to come fix it?" or "When can I expect him?")