Beamforming technique at the ground station is known to be effective in obtaining coverage extension or SNR gain for communication with unmanned aerial vehicle (UAV). When a UAV moves, periodic beam tracking is necessary to maintain beam gain. In order to track beams for multiple UAVs, the ground station needs to receive different preamble sequences from multiple UAVs. In this paper, a preamble sequence design technique is proposed for beam tracking in a GMSK-based communication system with multiple UAVs. Hadamard sequence is considered for the design of preamble sequence due to its ideal cross-correlation property. A preamble sequence appropriate for a GMSK communication system with multiple UAVs is proposed after analyzing the properties of received signal in a GMSK system with the input of Hadamard sequence.