The present study aimed to evaluate the effect of the agroecological zone, host age, and gender on the prevalence and faecal egg load of gastrointestinal parasites (GIPs) for six months (July to December) in the Maseru and Quthing districts, Lesotho. A total of 1919 faecal samples were examined using the McMaster technique. The data were analyzed through generalized estimating equations (GEE) under the binary logistic regression model to determine the significant differences for the GIPs prevalence. Moreover, faecal egg counts (FEC) data were analyzed for repeated measures using GEE. In total, three types of GIPs, namely nematodes, coccidia, and cestodes were identified in this study. The overall prevalence rates of nematodes, coccidia, and cestodes were 53.9%, 46.5%, and 4.3% in the Maseru district, respectively. Furthermore, the Quthing district indicated the prevalence rates of 65.0%, 38.2%, and 0.9% for nematodes, coccidia, and cestodes, respectively. In the Maseru district, the overall faecal egg counts for nematodes, coccidia, and cestodes were within the ranges of 0-20.3, 0-90, and 0-600 eggs per gram, respectively. Additionally, the faecal egg counts in the Quthing district ranged from 0 to 8.000, 6.700, and 2.000 eggs per gram for nematodes, coccidia, and cestodes, respectively. The majority of the Merino sheep (>69%) in both districts had lower faecal egg counts (100-800) per gram. The agroecological zone affected the nematode infestation in both districts. Coccidia in the Quthing was higher in the mountain areas. In the Maseru district, the nematode infestation was not age-dependent; however, in the Quthing district, the prevalence was higher in juveniles, compared to adults. Age and gender did not affect the prevalence and faecal egg counts of nematodes and coccidia. The coccidian faecal egg loads were higher in females, compared to males. Merino sheep in Lesotho are mostly infected with gastrointestinal nematodes and protozoal coccidia, which could have a tremendous impact on their health and productivity. It is, therefore, of significant importance to develop the deworming strategy for sheep of different age and gender groups in different agroecological zones.