To predict our brain disorders, EEG signals need to be analyzed. However, most EEG signals were affected by different kinds of noise during their acquision. So, signal analysis become most difficult due to the contamination of various noise. An appropriate technique is necessary to remove the noise from the signal. Wavelet Transform is one the most widely used technique for removing the noise from EEG signals. Wave atom is one of the new multiscale-multidirectional transforms, which is better than both wavelet as well as curvelet transforms. This wave atom transform has good orientation characteristic by which it preserves the edges in an efficient manner. This paper introduced a new method for denoising of EEG signal by shift-based cycle spinning on wave atom transform. Cycle spinning is a technique can be used to enhance the capability of wave atoms. An original EEG signals from public EEG database were used for this experiment. The results are analysed based on the performance measurements like SNR and MSE. The experimental results show that cycle spinning technique with appropriate shifts could be the better choice to denoise an EEG signals.