Individual septic tanks are the most common means of on-site sanitation in Malaysia, but they result in a significant volume of septage. A two-staged vertical flow constructed wetlands (VFCWs) system for the treatment of septage was constructed and studied in Sarawak, Malaysia. Raw septage was treated in the first stage wetlands, and the resulting percolate was fed onto the second stage wetlands for further treatment. Here, the effects of a batch loading regime on the contaminant removal efficiency at the second stage wetlands, which included palm kernel shell within their filter substrate, are presented. The batch loading regime with pond:rest (P:R) period of 1:1, 2:2 and 3:3 (day:day) was studied. The improvement of the effluent redox condition was evident with P:R = 3:3, resulting in excellent organic matters (chemical oxygen demand and biochemical oxygen demand) and nitrogen reduction. The bed operated with P:R = 1:1 experienced constant clogging, with a water layer observed on the bed surface. For the P:R = 3:3 regime, the dissolved oxygen profile was not found to decay drastically after 24 hours of ponding, suggesting that the biodegradation mainly occurred during the first day. The study results indicate that a suitable application regime with an adequate rest period is important in VFCWs to ensure efficient operation.