Control barrier functions (CBFs) have recently been introduced as a systematic tool to ensure safety by establishing set invariance. When combined with a control Lyapunov function (CLF), they form a safety-critical control mechanism. However, the effectiveness of CBFs and CLFs is closely tied to the system model. In practice, model uncertainty can jeopardize safety and stability guarantees and may lead to undesirable performance. In this paper, we develop a safe learning-based control strategy for switching systems in the face of uncertainty. We focus on the case that a nominal model is available for a true underlying switching system. This uncertainty results in piecewise residuals for each switching surface, impacting the CLF and CBF constraints. We introduce a batch multi-output Gaussian process (MOGP) framework to approximate these piecewise residuals, thereby mitigating the adverse effects of uncertainty. A particular structure of the covariance function enables us to convert the MOGP-based chance constraints CLF and CBF into second-order cone constraints, which leads to a convex optimization. We analyze the feasibility of the resulting optimization and provide the necessary and sufficient conditions for feasibility. The effectiveness of the proposed strategy is validated through a simulation of a switching adaptive cruise control system.