This article presents a portable and programmable frequency measurement system (PrO-FMS) with 0.1-ppm RMSE resolution over a measurement time interval of 33.2 s for bulk-acoustic resonator applications. PrO-FMS has a feature of choosing a frequency estimation method and accordingly the sampling frequency, which is programmable. Five frequency estimation methods, Candan, Djukanovic, Prony, M-Pisarenko, and zero crossing interpolation methods, are reviewed for high-resolution frequency measurement. PrO-FMS can also be reconfigured to select a particular resonance mode over a range of 1-10 MHz. Measurement results are provided for two different commercial quartz crystals and a microfabricated in-plane bulk acoustic resonator in two different modes of resonance. The results of these estimation methods are compared with a standard commercial tabletop frequency counter. Measurement results show that PrO-FMS can achieve a resolution of 0.1 ppm RMSE. For the same gate time, PrO-FMS provides better resolution than standard tabletop frequency counter. This article also provides a study on the behavior of the five different frequency estimation methods for short-and long-term measurements for quartz crystals and bulk acoustic resonator in two different modes.