Gastrointestinal parasites are the major threats to camel production and productivity losses in pastoral communities of Ethiopia. A cross-sectional study was conducted starting from September 2017 to April 2018 in Administrative Zone three of the Afar Region, Ethiopia. The objectives of the study were to determine the prevalence and associated risk factors for gastrointestinal parasites in camels. Fecal samples were collected aseptically from the rectum, and floatation and sedimentation techniques were used to identify the parasite in the laboratory. Out of 450 fecal samples collected from camels, 76% (71.8–79.7) of them were harboring at least one parasite in their gastrointestinal tract. The majority of infections were mixed parasitic infections. Nematodes, trematodes, protozoa, and cestodes were encountered in descending order of their prevalence. Strongyle, Trichostrongylus, and Haemonchus eggs were the most frequently encountered parasite eggs. The occurrence of parasite eggs was statistically significantly associated with the age of the camels and their origin (
p
value <0.05). Older camels in the Amibara district were the most likely affected groups (OR = 2.34 (1.01–5.44)). However, the sex of the camels was not associated with the prevalence of gastrointestinal parasites. Generally, the present study indicated a high prevalence of parasites which were economically important in the study area. So, awareness about the magnitude and control options should be given to the camel owners in the study area. Infected animals should be treated with effective anthelmintics like albendazole and ivermectin. Routine and scheduled deworming and good husbandry practices should be implemented. Further study on seasonal occurrences and species identification of the parasites should be studied.