The primary aim of this retrospective study was to assess differences in the pathogens causing surgical site infections (SSIs) following craniectomies/craniotomies and open spinal surgery. The secondary aim was to assess differences in rates of SSI among these operative procedures. ANOVA tests with Bonferroni correction and incidence risk ratios (RRs) were used to identify differences in pathogens by surgical site and procedure using retrospective, de-identified records of 19,993 postneurosurgical patients treated between 2007 and 2020. The overall infection rates for craniotomy/craniectomy, laminectomy, and fusion were 2.1%, 1.1%, and 1.5%, respectively, and overall infection rates for cervical, thoracic, and lumbar spine surgery were 0.3%, 1.6%, and 1.9%, respectively. Craniotomy/craniectomy was more likely to result in an SSI than spine surgery (RR 1.8, 95% CI 1.4-2.2, p < 0.0001). Cutibacterium acnes (RR 24.2, 95% CI 7.3-80.0, p < 0.0001); coagulase-negative staphylococci (CoNS) (methicillin-susceptible CoNS: RR 2.9, 95% CI 1.6-5.4, p = 0.0006; methicillin-resistant CoNS: RR 5.6, 95% CI 1.4-22.3, p = 0.02); Klebsiella aerogenes (RR 6.5, 95% CI 1.7-25.1, p = 0.0003); Serratia marcescens (RR 2.4, 95% CI 1.1-7.1, p = 0.01); Enterobacter cloacae (RR 3.1, 95% CI 1.2-8.1, p = 0.02); and Candida albicans (RR 3.9, 95% CI 1.2-12.3, p = 0.02) were more commonly associated with craniotomy/craniectomy cases than fusion or laminectomy SSIs. Pseudomonas aeruginosa was more commonly associated with fusion SSIs than craniotomy SSIs (RR 4.4, 95% CI 1.3-14.8, p = 0.02), whereas Escherichia coli was nonsignificantly associated with fusion SSIs compared to craniotomy SSIs (RR 4.1, 95% CI 0.9-18.1, p = 0.06). Infections with E. coli and P. aeruginosa occurred primarily in the lumbar spine (p = 0.0003 and p = 0.0001, respectively). SSIs due to typical gastrointestinal or genitourinary gram-negative bacteria occur most commonly following lumbar surgery, particularly fusion, and are likely to be due to contamination of the surgical bed with microbial flora in the perianal area and genitourinary tract. Cutibacterium acnes in the skin flora of the head and neck increases risk of infection due to this microbe following surgical interventions in these body sites. The types of gram-negative bacteria associated with craniotomy/craniectomy SSIs suggest potential environmental sources of these pathogens. Based on the authors' findings, neurosurgeons should consider using a two-step skin preparation with benzoyl peroxide, in addition to a standard antiseptic such as alcoholic chlorhexidine for cranial, cervical, and upper thoracic surgeries. Additionally, broader gram-negative bacterial coverage, such as use of a third-generation cephalosporin, should be considered for lumbar/lumbosacral fusion surgical antibiotic prophylaxis.