We report on a frequency-tunable terahertz pulse train generated from a rectangular GaP waveguide emitter pumped by a pulse width tunable femtosecond photonic crystal fiber amplifier. The THz frequency can be tuned by varying the pump pulse duration. The dispersion of the emitter can be controlled via the geometry of the waveguide, and the coherent buildup length can be increased to scale up the output power. Waveguides with different cross sections can be used to tune the THz spectrum. Combined with the pump pulse duration tuning technique, THz pulses with a precisely tunable frequency can be obtained. In the experiment, tunable THz radiation is obtained from a GaP waveguide emitter with a cross section of 1 mm0.7 mm. Finally, a GaP emitter array is designed to achieve a wider tuning range.