Tuberculosis (TB) in children is a critical public health issue. In Bohol, Philippines, we found a high tuberculin skin test (TST)-positive prevalence (weighted prevalence = 6.4%) among 5476 children (<15 years) from 184 villages, with geographically isolated communities having prevalence as high as 29%. Therefore, we conducted a geospatial and hot spot analysis to examine the association between villages with high TST-positive prevalence (⩾6.5%) and access to medical care (distance (in kilometres and minutes of travel time) to the municipal Rural Health Units (RHU)), access to healthcare resources (distance to Provincial Health Office (PHO)) and socioeconomic determinants of health. Hot spot analysis revealed significant clusters of TST-positive prevalence in villages farthest from the PHO. Based on univariate analysis, the following variables associated with high prevalence were included in the multivariate model: minutes of travel time to the PHO, distance to the PHO, island villages and total deprivation based on socioeconomic indicators. In the final model, only distance to PHO in minutes was significant (P = 0.005). When evaluated further, greater than 1-hour drive significantly increased risk for TST-positivity (P = 0.003). Distance to healthcare resources likely increases the risk of TB transmission within the community. Expanding TB control efforts to geographically isolated areas is critical.