Individuals infected with human immunodeficiency virus (HIV) have a high chance of developing parasitic intestinal infections. The presence of zoonotic parasites in animal faeces is also believed to be evidence of readily available sources of infection for humans with these parasites. This study therefore evaluates the prevalence of intestinal parasitic infections among HIV-infected patients and domestic animals. A cross-sectional hospital-based study was carried out at three antiretroviral therapy clinics in Ekiti State, Southwest, Nigeria between February 2018 and December 2019. A total of 330 HIV-infected patients and 77 domestic animals (within their environment) were studied. Faeces were collected and processed using formol-ether concentration and modified Ziehl-Neelsen techniques for the detection of intestinal parasites and Cryptosporidium oocysts, respectively. Socio-demographic and clinical data were collected using structured questionnaires. Fisher’s Exact Test statistical analysis was used to test the level of significance at p < 0.05. The overall prevalence of intestinal parasitic infections among the study population of HIV patients and their pets were 15.5% and 12% respectively. The most predominant parasitic infections amongst the HIV patients was Cryptosporidium sp., (49.0%), while Taenia and Hymenolepis sp. were least with 5.9% each. The CD4 count < 200 (OR: 10.2, 95% CI: 4.3–23.7), and diarrhoea (OR: 7.0, 95% CI: 3.2–17.8) were detected to be the significant associated variables with Cryptosporidium infection. Cryptosporidium sp., (32.1%), Ancylostoma caninum (7.1%) and Toxocara canis (7.1%) were parasites of zoonotic potential detected in animals of participants. Improving public health measures that would emphasize personal hygiene and regular deworming of immunocompromised pets by certified veterinarians is recommended.