Introduction: Diarrhea is one of the major complications occurring in over 90% of human immunodeficiency virus (HIV)-infected individuals in developing countries. Coccidian group of parasitic infections remain the standout opportunistic pathogens in many parts of the world. Aim: The objective was to understand the profile of diarrheagenic parasites in HIV/AIDS patients along with analysis of the changing trends in the profile of parasitic diarrhea with special context to coccidian parasitic infections. Methodology: A cross-sectional study was performed at “ID CENTRE FOR NORTHEAST,” Shillong, from January 2014 to October 2017. Stool samples collected were observed microscopically for parasites both on direct and concentrated stool samples under ×10 and ×40 magnification. Modified acid-fast staining was used for the detection of coccidian parasites. All statistical analyses were performed using IBM SPSS software, Version 24.0. Results: The prevalence of intestinal parasitic infections was 40.99%, coccidian parasitic infection accounted for 85.13% of total intestinal parasitic infections. Cryptosporidium parvum was the most common cause of diarrhea (70.64%), followed by Cystoisospora belli (23.81%) and Cyclospora spp. (5.55%). Trend analysis of coccidian etiology during the study revealed a significant rise in the positivity of Cryptosporidium spp. and a decrease in the Cystoisosporiasis belli infection. The common noncoccidian parasites identified include hookworm (8.1%) followed by Ascaris lumbricoides (4.7%). Conclusion: The magnitude of parasitic infections is considerably high among the HIV/AIDS patients in Northeast India, and it is essential for screening and periodic monitoring of all the HIV patients for coccidian parasites by stool microscopy.