It has long been proposed that emotionally “prepared” (i.e., fear-related) stimuli are privileged in the unconscious acquisition of conditioned fear. However, as fear processing is suggested to highly depend on the coarse, low-spatial-frequency (LSF) components of the fear-related stimuli, it is plausible that LSF may play a unique role in the unconscious fear conditioning even with emotionally neutral stimuli. Here, we provided empirical evidence that, following classical fear conditioning, an invisible, emotionally neutral conditioned stimulus (CS+) with LSF, but not with high spatial frequency (HSF), can rapidly elicit stronger skin conductance responses (SCRs) and larger pupil diameters than its CS− counterpart. In comparison, consciously perceived emotionally neutral CS+ with LSF and HSF elicited comparable SCRs. Taken together, these results support that the unconscious fear conditioning does not necessarily entail emotionally prepared stimuli but prioritizes LSF information processing and highlight the crucial distinctions between the unconscious and the conscious fear learning. These findings not only coincide with the postulation that a rapid, spatial-frequency-dependent subcortical route is engaged in unconscious fear processing but also suggest the existence of multiple routes for conscious fear processing.