Predicting the battery’s end-of-life (EOL) with uncertainty quantification is critical for ensuring system safety and reliability. This paper presents a hybrid framework for battery EOL prediction and its uncertainty assessment based on Gaussian process regression (GPR) and Kalman filter (KF). First, a KF-based empirical-model-free state tracking phase is applied for the available partial battery degradation data. Then, the original time series forecasting problem of degradation curves is converted to the prediction of the virtual degradation rate and acceleration. Next, the prediction of the virtual degradation rate and acceleration is executed by the iterative GPR multi-step ahead prediction strategy with moving sliding windows. Finally, the uncertainty assessment is carried out based on the sliding window length determination process. The effectiveness of our proposed method is validated on the open-source lithium-ion battery degradation dataset from the University of Oxford. Extensive EOL prediction tests have been carried out from 40% (early-stage), 60% (middle-stage), and 80% (late-stage) of the dataset, respectively. Compared with the popular EOL prediction method within particle filter framework, the predicted mean EOL cycle by our method is closer to the true value with a smaller range of prediction uncertainty.