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A Model Predictive Control Based Trajectory Tracking (MPCTT) system for small unmanned helicopters is presented. A linear model predictive controller is used to take advantage of the fast algorithms available to solve convex optimization problems. The proposed MPCTT system is compared with a velocity tracking and a position tracking system implemented with classical PIDs from previous research work. Obtained simulation results demonstrate the superiority of the proposed MPCTT approach, generating a substantially less control effort in order to track waypoint trajectories. The unmanned helicopter used for the proposed MPCTT system is considered as a (linearized) linear state-space model obtained for hovering and slow motion; however, as shown, the MPCTT is robust enough to perform trajectory tracking under a cruise flight mode, too.