Are you meaning a combustion engine? If that’s the case, you should be able to but you’ll have to be conscious of vibration transmitted to the Pixhawk.
I do have a pixhawk working on a petrol engine fixed wing UAV.
I am not quite worried about the vibrations. I just got this in my mind, as, on VTOL ardupilot website it has recommendation for only 4 models and all are electric. That led me to ask this question - whether Pixhawk can be set for Engine powered VTOL UAVs or not.
Its just that I will have to turn ON the engine first, then BLDC motors (for Quad) and takeoff vertically.