Background Pre-school-aged children are always excluded in mass intervention policies for control of soil-transmitted helminths in Nigera. The need for evidence on infectivity of children in this age group cannot be overemphasized. This study seeks to determine the prevalence of STH among 103 children who are less than 2 years of age in an urban and rural area of Ogun State, Nigeria. This study through questionnaire administration also obtained relevant demographic information and hygiene behavior from parents of children recruited to this study. Results The overall prevalence of 69.9% was recorded, with Ascaris lumbricoides occurring as the most prevalent helminth (68.0%). This was followed by Hook worm (49.5%) and Trichris trichuria (18.5%). A significant increase in prevalence of hookworm was observed with increase in age (p < 0.05). Generally, A. Lumbricoides was found to be more prevalent as a single infection in the study population. Most of the T. Trichuria and hookworm infections were either in co-infections infections with A. Lumbricoides. The prevalence of A. Lumbricoides and Hookworm were significantly high in rural community when compared with urban (p < 0.05). Poor hygiene practices were common among the study participants. Conclusions The prevalence of STH infection is incredibly high in this age group that was for a long time considered as less important when it comes to burden due to STH. Therefore, there is a need to include them into future plans for control interventions.