Introduction Surgical site infection (SSI) is a significant cause of postoperative morbidity and mortality. Effective preoperative antisepsis is a recognised prophylactic, with commonly used agents including chlorhexidine (CHG) and povidone-iodine (PVI). However, there is emerging evidence to suggest an additional benefit when they are used in combination. Methods We analysed data from our prospective SSI database on patients undergoing clean cranial neurosurgery between October 2011 and April 2014. We compared the case-mix adjusted odds of developing a SSI in patients undergoing skin preparation with CGH or PVI alone or in combination. Results SSIs were detected in 2.6% of 1146 cases. Antisepsis with PVI alone was performed in 654 (57%) procedures, while 276 (24%) had CHG alone and 216 (19%) CHG and PVI together. SSIs were associated with longer operating time (p<0.001) and younger age (p=0.03). Surgery type (p<0.001) and length of operation (p<0.001) were significantly different between antisepsis groups. In a binary logistic regression model, CHG and PVI was associated with a significant reduction in the likelihood of developing an SSI (adjusted odds ratio [AOR] 0.12, 95% confidence interval [CI] 0.02–0.63) than either agent alone. There was no difference in SSI rates between CHG and PVI alone (AOR 0.60, 95% CI 0.24–1.5). Conclusions Combination skin preparation with CHG and PVI significantly reduced SSI rates compared to CHG or PVI alone. A prospective, randomized study validating these findings is now warranted.