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Time-of-flight (TOF) measurement using a femtosecond laser has nanometer precision over long distance without any ambiguity problem. For commercial use of the high-resolution distance meter, the electronic parts including control, analysis and data acquisition should be compact and rugged as well as lasers and optics. Among the electronic parts, a frequency counter is measuring frequency of the repetition rate of the laser which is directly converted into distance information. In this paper, a compact and cost-effective frequency counter was developed using an 8-bit microcontroller with a Rubidium clock referencing for securing long-term stability. The frequency counter showed measurement error of 0.02 Hz and a measurement stability of 6×10-4 (at 1 s) and 5×10-6 (at 100 s) making it potentially applicable to the TOF measurement principle.