Background This study examined caregiver assessment of executive functioning (EF) in perinatally HIV-infected (PHIV) and perinatally HIV-exposed but uninfected (PHEU) Kenyan children, and explored the extent to which various biopsychosocial factors influence EF outcomes. Methods Children aged 3–5 years that were PHIV ( n  = 43), PHEU ( n  = 52), or HIV-unexposed uninfected (HUU, n  = 58) and their caregivers were enrolled in this study. EF was measured using the Childhood Executive Functioning Inventory. Caregivers’ common mental disorders (CMDs) and parenting behaviour were evaluated using the Shona Symptoms Questionnaire (SSQ) and a parenting behaviour scale, respectively. We used analyses of variance to assess group differences in EF scores and a hierarchal linear regression model to explore covariates associated with EF outcomes. Results Overall, we observed significant negative effects of HIV exposure on EF scores, F (2, 149) = 8.591, p  < 0.001. Compared to HUU children, PHIV children performed worse in working memory [mean difference (MD), 2.89 [95% CI: 0.65–5.14] p  = 0.008], inhibitory control [MD , 2.47 (95% CI: 0.55–4.40), p   =  0.008], and composite EF [MD, 5.37 (95% CI: 1.97–8.76), p  = 0.001]. PHEU children showed poorer performance in working memory [MD, 3.24 (95% CI: 1.11–5.37), p   =  0.001] and composite EF [MD, 4.97 (95% CI: 1.75–8.19) , p  = 0.001]. The observed EF impairment was strongly associated with caregivers’ CMDs and advanced HIV disease in children. Conclusion Our study suggests that caregivers can observe overt executive dysfunction in children perinatally exposed to HIV. These findings underscore the importance of antiretroviral therapy adherence in PHIV children and the provision of psychosocial support to caregivers of HIV-exposed children to improve EF outcomes.