Systems and methods for automatic detection and compensation of frequency offset in point-to-point communication. A burst mode clock and data recovery (CDR) system comprises input data received at a first frequency and a reference clock operating at a second frequency. A master phase-locked loop (PLL) comprising a first gated voltage controlled oscillator (GVCO) is configured to align the phases of reference clock and the input data, and provide phase error information and a recovered clock. A second GVCO is controlled by the recovered clock to sample the input data. A frequency alignment loop comprising a feedback path from the second GVCO to the master PLL is configured to use the phase error information to correct a frequency offset between the first frequency and the second frequency.