Total sleep deprivation (TSD) negatively affects cognitive function. Previous research has focused on individual variation in cognitive function following TSD, but we know less about how TSD influences the lateralization of spatial working memory. This study used event-related-potential techniques to explore asymmetry in spatial-working-memory impairment. Fourteen healthy male participants performed a two-back task with electroencephalogram (EEG) recordings conducted at baseline and after 36 h of TSD. We selected 12 EEG points corresponding to left and right sides of the brain and then observed changes in N2 and P3 components related to spatial working memory. Before TSD, P3 amplitude differed significantly between the left and right sides of the brain. This difference disappeared after TSD. Compared with baseline, P3 amplitude decreased for a duration as extended as the prolonged latency of N2 components. After 36 h of TSD, P3 amplitude decreased more in the right hemisphere than the left. We therefore conclude that TSD negatively affected spatial working memory, possibly through removing the right hemisphere advantage.