ABSTRACTAccurate software reliability prediction is significant to software quality assurance. However, the rapid development and evolution of modern software pose more challenges for accurate software quality assessment. With the rapid development of machine learning and intelligent algorithms, data‐driven nonparametric models have gradually attracted increasing attention with outstanding prediction performance. However, we found that there may exist some prediction lags caused by the autocorrelation and nonstationarity of software fault data in the prediction of nonparametric models affecting their performance. To address this problem, we proposed an adaptive gated recurrent unit‐based encoder‐decoder model (ED‐GRU) with ensemble empirical mode decomposition (EEMD), effectively reducing prediction lags and performing accurate software fault number prediction. The autocorrelation and nonstationarity of fault data are first reduced by using first‐order difference and EEMD to clearly characterize the changing trend of the data. The frequency‐specific ED‐GRU networks are then combined to adaptively learn the nonlinear fluctuation trend of fault data under different frequency scales and obtain accurate prediction final results after aggregation. Experiments on eight public datasets showed that the proposed EEMD‐ED‐GRU‐PF model could effectively reduce the prediction lags and achieve the best prediction performance compared with four nonparametric and five parametric baseline methods in all datasets. Therefore, the proposed method can effectively and stably reduce the prediction lag to significantly improve the prediction accuracy. In this way, developers can accurately evaluate the current quality of the software and provide valuable guidance for software development and maintenance.