Epstein-Barr virus (EBV) and human papillomavirus (HPV) are common oncoviruses that infect similar anatomical sites, persist as latent infections, and contribute to oncogenesis. However, the role of EBV as a cofactor in HPV infection outcomes remains unclear. This study assessed the implications of EBV serology on oral and genital HPV infections in a longitudinal setting. The study included 280 women from the Finnish Family HPV cohort, followed for three years. Oral, genital, and blood samples were collected at baseline and 12-, 24-, and 36-month follow-ups. EBV-IgG antibodies to Zebra, EA-D, EBNA-1, and VCAp18 proteins were analyzed using multiplex serology, and HPV genotyping was performed with the Multimetrix® assay. Among the 280 women, 98.2% (n = 275) were seropositive for at least two EBV antibodies, with stable antibody levels over the follow-up. Self-reported atopy increased the likelihood of high Zebra and VCAp18 antibody levels OR 2.11 (95%CI 1.07–4.17) and OR 2.45 (95%CI 1.24–4.83). No clear associations between EBV serology and longitudinal oral and genital HPV outcomes were found. In conclusion, nearly all women tested positive for EBV antibodies, however, no notable implications between EBV antibody levels and longitudinal outcomes of oral and HPV infection outcomes could be determined.