Many failure mechanisms of machinery are closely related to the behavior of condition monitoring (CM) signals. To achieve a cost-effective preventive maintenance strategy, accurate remaining useful life (RUL) prediction based on the signals is of paramount importance. However, the CM signals are often recorded at different factories and production lines, with limited amounts of data. Unfortunately, these datasets have rarely been shared between the sites due to data confidentiality and ownership issues, a lack of computing and storage power, and high communication costs associated with data transfer between sites and a data center. Another challenge in real applications is that the CM signals are often not explicitly specified \textit{a priori}, meaning that existing methods, which often usually a parametric form, may not be applicable. To address these challenges, we propose a new prognostic framework for RUL prediction using the joint modeling of nonlinear degradation signals and time-to-failure data within a federated learning scheme. The proposed method constructs a nonparametric degradation model using a federated multi-output Gaussian process and then employs a federated survival model to predict failure times and probabilities for in-service machinery. The superiority of the proposed method over other alternatives is demonstrated through comprehensive simulation studies and a case study using turbofan engine degradation signal data that include run-to-failure events.