The urban populations of pets, mainly dogs and cats, have been growing in recent years and, consequently, human–animal relationships have become increasingly closer. However, pets are vulnerable to infection by various parasites, as well are their owners due to the zoonotic potential of these agents. This study aimed to assess the frequency and risk factors of intestinal parasites in dogs and cats attended at the Municipal Institute of Veterinary Medicine Jorge Vaitsman, Rio de Janeiro, Brazil, as well as georeferencing the parasitized animals. A total of 608 animals (400 dogs and 208 cats) were enrolled from August 2017 to November 2018. Fecal samples were obtained from the animal’s rectum during clinical examination. In addition, the owners of the enrolled dogs and cats were asked to complete an epidemiological questionnaire with questions about the animals’ general information, lifestyle, and handling. Fecal samples were subjected to sedimentation and centrifugal-flotation in sucrose solution techniques. The frequencies of intestinal parasites total in dogs and cats were 11.3% and 24.5%, respectively, with hookworms being the most detected parasites in dogs (8.3%) and Dipylidium caninum in cats (12.5%). Sex was the only variable that showed statistical differences in the canine population males being more often infected than female (p < 0.05), while street access was associated with parasitic infections in cats (p < 0.05). The results obtained in this study demonstrate the need to control parasitic infections in domiciled dogs and cats in different municipalities in the metropolitan region of the state of Rio de Janeiro, including residents in the northern, western and central areas.