Time series, including noise, non-linearity, and non-stationary properties, are frequently used in prediction problems. Due to these inherent characteristics of time series data, forecasting based on this data type is a highly challenging problem. In many studies within the literature, high-frequency components are commonly excluded from time series data. However, these high-frequency components can contain valuable information, and their removal may adversely impact the prediction performance of models. In this study, a novel method called Two-Level Entropy Ratio-Based Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (2LE-CEEMDAN) is proposed for the first time to effectively denoise time series data. Financial time series with high noise levels are utilized to validate the effectiveness of the proposed method. The 2LE-CEEMDAN-LSTM-SVR model is introduced to predict the next day’s closing value of stock market indices within the scope of financial time series. This model comprises two main components: denoising and forecasting. In the denoising section, the proposed 2LE-CEEMDAN method eliminates noise in financial time series, resulting in denoised intrinsic mode functions (IMFs). In the forecasting part, the next-day value of the indices is estimated by training on the denoised IMFs obtained. Two different artificial intelligence methods, Long Short-Term Memory (LSTM) and Support Vector Regression (SVR), are utilized during the training process. The IMF, characterized by more linear characteristics than the denoised IMFs, is trained using the SVR, while the others are trained using the LSTM method. The final prediction result of the 2LE-CEEMDAN-LSTM-SVR model is obtained by integrating the prediction results of each IMF. Experimental results demonstrate that the proposed 2LE-CEEMDAN denoising method positively influences the model’s prediction performance, and the 2LE-CEEMDAN-LSTM-SVR model outperforms other prediction models in the existing literature.