We describe a compact waveguide amplifier system that is suitable for optically pumping rubidium magnetometers. The system consists of an auto-locking vacuum-sealed external cavity diode laser, a semiconductor tapered amplifier and a pulsing unit based on an acousto-optic modulator. The diode laser utilises optical feedback from an interference filter to narrow the linewidth of an inexpensive laser diode to ~500 kHz. This output is scannable over an 8 GHz range (at 780 nm) and can be locked without human intervention to any spectral marker in an expandable library of reference spectra, using the autolocking controller. The tapered amplifier amplifies the output from 50 mW up to 2 W with negligible distortions in the spectral quality. The system can operate at visible and near infrared wavelengths with MHz repetition rates. We demonstrate optical pumping of rubidium vapour with this system for magnetometric applications. The magnetometer detects the differential absorption of two orthogonally polarized components of a linearly polarized probe laser following optical pumping by a circularly polarized pump laser. The differential absorption signal is studied for a range of pulse lengths, pulse amplitudes and DC magnetic fields. Our results suggest that this laser system is suitable for optically pumping spin-exchange free magnetometers.