Fear acquisition manifests in the development of conditioned fear responses (CRs), whereas a decrement in CRs as a consequence of unconditioned stimulus (UCS) omission is referred to as extinction learning. Time windows for CR scoring in physiological readouts are subject to discussion, especially regarding the subdivision of skin conductance responses (SCRs) into first- (FIR) and second-interval responses (SIR). However, distinct temporal CR trajectories within or across measures may reflect specific characteristics of the underlying associative processes. In this study, 41 participants underwent fear acquisition and extinction, while SCRs and pupillary responses were recorded and separated into different time bins to explore the temporal dynamics of CRs across both learning phases. For SCRs, we observed a shift from early (FIR) to late (SIR) time intervals during fear acquisition most likely reflecting subsequent learning processes, in which CS-UCS associations and their relative timing are formed. During extinction, only the FIR exhibited a CR decline and was thus able to track the learning progress. These results indicate that conditioned SCRs follow a dynamic temporal pattern that may be related to different learning dimensions. By contrast, pupillary CRs were generally better captured by a late pupillary response component, suggesting a rather stable temporal CR pattern for the pupil in both learning phases. Our findings underscore the importance of specifying CR quantification for different physiological readouts when evaluating learning performance in the context of fear acquisition and extinction and may motivate further investigation of time-specific CR patterns and their relation to specific associative dimensions.