Non-typhoidal Salmonella (NTS) infections remain a significant public health challenge especially in sub-Saharan Africa. NTS disease is endemic in Kenya and is associated with sporadic fatal outbreaks in several regions of the country with poor resource setting. Data is limited on background exposure of NTS in the population in endemic areas and the general immune status of the community most affected by NTS. The aim of the study was to determine the proportion of children exposed to Salmonella Enteritidis or Salmonella Typhimurium O antigen among the apparently healthy children and patients and the associated host and environmental factors among children attending selected healthcare facilities in Mukuru, Nairobi County, Kenya. A cross-sectional case-control study was conducted among patients and apparently healthy participants aged 0–5 years. Blood was collected and centrifuged to obtain serum. The serum was used to test for the presence of antibodies (IgA, IgG, IgM) against NTS using ELISA. A questionnaire was administered to obtain relevant demographic, socio-economic and healthcare utilization information. A total of 382 children were recruited into the study. The NTS seroprevalence was 12.6%. Among the apparently healthy participants, mean age of those exposed to NTS was 36 months and those not exposed was 27 months. Among patients, the mean age was 39 months and those not exposed was 30 months. The seroprevalence of NTS infection among the apparently healthy was significantly associated with cooking water, washing water and age of the child. Treating water using chlorine or boiling method was identified as being protective against contracting Salmonella Typhimurium/Enteritidis. Among the patients, the proportion of exposure was significantly associated with keeping animals and the chicken count. There is a high exposure to NTS among young children below five years of age and the population has developed immunity to the disease.