A compact single-photon counting module that can accurately control the bias voltage and hold-off time is developed in this work. The module is a microcontroller-based system which mainly consists of a microcontroller, a programmable negative voltage generator, a silicon-based single-photon avalanche diode, and an integrated active quench and reset circuit. The module is 3.8 cm × 3.6 cm × 2 cm in size and can communicate with the end user and be powered through a USB cable (5 V). In this module, the bias voltage of the single-photon avalanche diode (SPAD) is precisely controllable from −14 V ~ −38 V and the hold-off time (consequently the dead time) of the SPAD can be adjusted from a few nanoseconds to around 1.6 μs with a setting resolution of ∼6.5 ns. Experimental results show that the module achieves a minimum dead time of around 28.5 ns, giving a saturation counting rate of around 35 Mcounts/s. Results also show that at a controlled reverse bias voltage of 26.8 V, the dark count rate measured is about 300 counts/s and the timing jitter measured is about 158 ps. Photodetection probability measurements show that the module is suited for detection of visible light from 450 nm to 800 nm with a 40% peak photon detection efficiency achieved at around 600 nm.