In this paper, a system for time-frequency analysis of heart rate variability (HRV) using a fast windowed Lomb periodogram is proposed. Time-frequency analysis of HRV is achieved through a de-normalized fast Lomb periodogram with a sliding window configuration. The Lomb time-frequency distribution (TFD) is suited for spectral analysis of unevenly spaced data and has been applied to the analysis of HRV. The system has been implemented in hardware as an HRV processor and verified on FPGA. Simulations show that the proposed Lomb TFD is able to achieve better frequency resolution than short-time Fourier transform of the same hardware size. The proposed system is suitable for portable monitoring devices and as a biomedical signal processor on an system-on-chip (SOC) design.