While performing heart rate estimation of a user, if the user is in motion, a signal is measured and is likely to have noise data, which in turn affects accuracy of estimated heart rate value. Method and system for heart rate estimation when the user is in motion is disclosed. The system estimates value of a noise signal present in a measured PPG signal by performing a Principal Component Analysis (PCA) of an accelerometer signal collected along with the PPG signal. The system further estimates value of a true cardiac signal for a time window, based on value of the true cardiac signal in a pre-defined number of previous time windows. The system then estimates frequency spectrum of a clean PPG signal based on the estimated noise signal and the true cardiac signal. The system further performs heart rate estimation based on the clean PPG signal.