The first officer, who was second in command of the Dash 8 aircraft, needed medical help and was met by paramedics from an ambulance waiting on the ground at the airport.
A spokeswoman for the airline said the captain took action "quickly and efficiently" to land the plane safely, Manchester Evening News reports .
An ambulance and fire engine met the plane as it pulled up near the control tower.
The pilot was taken away on a stretcher by waiting paramedics on the ground
Passengers waiting in the terminal saw the drama unfold. One said: "I was sat waiting to board my own flight and saw the ambulances and fire engine next to the Flybe plane.
"I then saw a person being stretchered off into the ambulance. I thought it must be serious because of how many paramedics there were."
The 44 passengers on board the flight, which was scheduled to take two hours, were put on a later flight to their Channel Island destination.
A spokeswoman for Flybe said: "Flybe can confirm that the flight en route from Inverness to Jersey landed safely after diverting to Manchester due to a medical situation in the cockpit.
"The captain quickly and efficiently took the necessary action and followed all required precautionary safety procedures to ensure the continued safe operation of the aircraft. On landing, the aircraft taxied to stand where it was met by local medical services.
"All 44 passengers disembarked as normal and will be re-accommodated on another flight. Flybe sincerely apologises to those passengers inconvenienced and will do everything possible to get them to their destination without further undue delay.
"All airlines train their crew to be prepared for all possible incidents, however rare, including that of a crew member becoming incapacitated during flight.
"Flybe crews are highly trained professionals and such procedures are reinforced on a regular basis, the safety of its passengers and crew remaining its highest priority at all times."