The purpose of this paper is to design a PID controller for a detailed nonlinear model of a custom-made quadcopter and utilise the power requirements in designing a proton exchange membrane (PEM) fuel cell system. The first principles methodology to commence with unmanned aerial vehicle architecture is delineated. The empirical actuator response of the brushless DC (BLDC) is obtained which further adds accuracy to the mathematical model of the system. The paper also presents simulations for nonlinear open loop and closed loop feedback with PID controller. The controller gains are obtained from the simulations for hover flight mode. The experimental implementation of battery powered quadcopter is validated with simulation results of PID control design. Finally, for the designed quadcopter, a mathematical model of a PEM fuel cell system to replace battery-specific power requirements is obtained. The key limitation of this paper is the absence of experimental data for fuel cell model due their high cost and low-availability.