Background: The backbone of Kenya’s soil-transmitted helminthiasis control program is the periodic distribution of anti-helminthic preventive chemotherapy (PC). PC distribution has been conducted since 2012 through the National School-Based Deworming Programme, which deworms school-age children (SAC, 5–14 years) living in areas at high risk for soil-transmitted helminth (STH) infections. After nearly a decade of deworming, the Ministry of Health sought to generate evidence for program monitoring by estimating the prevalence and intensity of STH infection in Narok and Bomet counties among at-risk groups: preschool-aged children (PSAC, 2–4 years), SAC, and women of reproductive age (WRA, 15–49 years), of which only SAC are covered by the deworming program. Methods: During August and December of 2021, we conducted cross-sectional, population-based household surveys in Narok and Bomet counties, using multi-stage, cluster random sampling among resident PSAC, SAC, and WRA. Individual and household questionnaires were administered using an electronic mobile platform. Stool samples were collected and tested for roundworms ( Ascaris lumbricoides ), hookworms ( Necator americanus, Ancylostoma duodenale ), and whipworms ( Trichuris trichura ) using the Kato-Katz method. Results: Stool samples were provided by 1,062 PSAC, 1,922 SAC, and 364 WRA. Results indicated that the prevalence of any STH infection in Bomet county was similar among SAC (16.2% [upper 95% design-corrected confidence interval [U95% CI]: 23.1%]) and PSAC (15.8% [U95% CI: 21.7%]). In Narok county, STH prevalence was marginally higher among PSAC (12.8% [U95% CI: 18.2%]) compared to SAC (11.3% [U95% CI: 16.2%]). Moderate-to-high intensity infection prevalence among PSAC and SAC exceeded the morbidity elimination threshold of 2% in both counties. A. lumbricoides and T. trichura were most identified; few hookworm infections were detected. Conclusions: STH infections remain a public health problem in Narok and Bomet counties. There may be a need to expand PC distribution to include risk groups beyond SAC during deworming exercises, as envisioned in the Breaking Transmission Strategy, to hasten progress toward the achievement of STH as a public health problem.