Approaches for predicting financial markets, including conventional statistical methods and recent deep learning methods, have been investigated in many studies. However, financial time series data (e.g., daily stock market index) contain noises that prevent stable predictive model learning. Using these noised data in predictions results in performance deterioration and time lag. This study proposes padding-based Fourier transform denoising (P-FTD) that eliminates the noise waveform in the frequency domain of financial time series data and solves the problem of data divergence at both ends when restoring to the original time series. Experiments were conducted to predict the closing prices of S&P500, SSE, and KOSPI by applying data, from which noise was removed by P-FTD, to different deep learning models based on time series. Results show that the combination of the deep learning models and the proposed denoising technique not only outperforms the basic models in terms of predictive performance but also mitigates the time lag problem.