This study investigated the overall prevalence of Haemonchus contortus infection in sheep and goats from five purposively selected subdivisions (sectors) of Nyagatare district from January to December 2014, after a high prevalence of gastrointestinal parasites and generalized poor productivity was reported in small ruminants in some districts of Rwanda. Faecal egg counts (FEC) were performed using the Modified Wisconsin Sugar Floatation method and the Fluorescent-labeled peanut-lectin agglutination test while enumerations, as log (FEC), were done using the modified McMaster method. The overall prevalence of H. contortus infection in sheep and goats was 75.7% (n=949). The overall prevalence of H. contortus infection in sheep (83.4%, n=314) was higher than in goats (71.8%, n=635) (Odds Ratio [OR] 1.98, 95% Confidence Interval [CI]: 1.40-2.79, and p≤0.001). The prevalence of H. contortus infection in female goats (74.2%) was higher than in male goats (64.3%) (OR 1.60, 95% CI: 1.09-2.36, and p=0.01). The prevalence of H. contortus infection in goats from Nyagatare was higher than in goats from Matimba (OR 3.25, 95% CI: 1.76-5.99, and p≤0.001) and from Katabagemu (OR 3.67, 95% CI: 2.04-6.59, and p≤0.001). The prevalence of H. contortus infection in goats from Karangazi was higher than in goats from Matimba (OR 4.72, 95% CI: 2.40-9.28, and p≤0.001). The overall mean monthly log (FEC) for H. contortus in sheep and goats were highest in April (18.9±0.2 and 14.05±0.1, respectively) and October (19.25± 0.2 and 13.75±0.1, respectively). Though, overall, sheep in Nyagatare district were at greater risk of H. contortus infection and goats from Nyagatare and Karangazi sectors were paradoxically at greater risk of H. contortus infection. It was also apparent that young female goats were at greater risk of H. contortus infection than young male goats. H. contortus infection is endemic in small ruminants in Nyagatare district and possibly other districts in Rwanda. Targeted selective treatment (TST) using FAMACHA with emphasis on low-lying swampy pastures and appropriate anthelmintic drugs may be the most economically viable solution in the short term. In the long term breeding of H. contortus resistant small ruminants and strategic grazing using the concept of refugia may bring about considerable relief from H. contortus infection in Nyagatare district, in particular, and Rwanda at large.