The World Health Organization has selected Malawi as one of three sites to pilot the roll-out of RTS,S/AS01 in phase 4 trials. As policy discussions for the expanded use of RTS,S/AS01 continue, it will be critical to determine the performance of the vaccine according to seasonal patterns of malaria transmission in regions of Africa. Given waning vaccine efficacy over time, this secondary analysis demonstrates that administering the vaccine to children in the months prior to malaria season could maximize impact of the vaccine. We followed children (5-17 months) and infants (6-12 weeks) assigned to one of three groups: (1) vaccine with four doses; (2) vaccine with three doses; (3) control. The primary endpoint was defined as episodes of clinical malaria. During the 4-years of follow-up, 658 of 1544 (42.6%) children and infants had at least one episode of clinical malaria. With each 1-inch increase in rainfall per month there was an associated increase in the rate of malaria by 12.6% (95% CI 9.6%, 15.6%, P < 0.0001) among children and 15.9% (95% CI 12.8%, 18.9%, P < 0.0001) among infants. There was no evidence of effect modification of vaccine efficacy by precipitation (89% power).