Background: Schistosomiasis (SCH) and soil transmitted helminthiasis (STH) have been targeted for elimination as a public health problem (EPHP) within the World Health Organization (WHO)’s Roadmap for Neglected Tropical Diseases (NTDs) 2021–2030. One of the global strategies for the control and elimination of these diseases is the mass administration of praziquantel and albendazole/mebendazole without prior individual diagnosis. To measure the progress towards the 2030 target, we conducted an assessment to determine the impact of the 3–5 rounds of annual mass drug administration among school age children in Ekiti State. Such scientific insights into the impact of these treatments will facilitate improved planning and targeting of resources towards reaching the last mile. Methodology: This assessment was conducted in 16 local government areas (LGAs) of Ekiti State between October and November 2023. Samples were collected from pupils in 166 primary and junior secondary schools across 166 wards of the State. Urine and stool samples were collected from 7670 pupils of ages 5 to 14 years, following standard laboratory procedures. Urine membrane filtration techniques were used for urine preparation while the Kato–Katz technique was used for stool preparation. A novel AiDx digital microscope was used to examine the presence of any ova in the prepared specimen. Parasite ova in urine were reported as the number of ova/10 mL of urine, and were categorized as light infection (˂50 ova/10 mL of urine) or heavy infection (>50 ova/10 mL of urine) while ova of parasites in stool samples were reported as eggs per gram of stool (EPG) and categorized into light, moderate and heavy infection. Results: Overall, 0.76% (0.56–0.95) at 95% CI of the 7670 respondents were infected with Schistosomia haematobium. No Schistosoma mansoni infection was recorded in the study. Similarly, 3.9% (3.43–4.29) at 95% CI were infected with STHs. The overall prevalence of schistosomiasis had significantly reduced from 8.2% in 2008 to 0.8%, while the overall prevalence of STHs significantly reduced from 30.9% to 3.9% with Ascaris lumbricoides being the dominant species of STH. In the 16 LGAs assessed, Ekiti West had the highest S. haematobium prevalence of 4.26%. Ise/Orun and Oye ranked second and third with a prevalence of 3.48% and 2.40% respectively, while all other LGAs had <1% prevalence. The prevalence of STHs was highest in Ekiti-West with a prevalence of 10.45% while Emure and Ikole Local Governments had the lowest prevalence of 0.31% and 0.38%, respectively. There was no significant difference in the prevalence of schistosomiasis between male (0.76%) and female (0.75%) as p ≥ 0.05. Similarly, the difference in prevalence for STH among males (3.95%) was not significantly different from their female counterparts (3.77%), p ≥ 0.05. Conclusions: Based on the WHO guidelines, this study demonstrated that only three LGAs require continued MDA every 2/3 years, seven require only surveillance while six are now non-endemic for schistosomiasis. Similarly, two of the LGAs require one round of MDA yearly, eight LGAs need one round of MDA every two to three years and six LGAs are now below the treatment threshold and no longer require treatment for STH.