Intestinal parasites of dogs and cats may affect their health with a significant zoonotic risk to public health. Therefore, establishing an efficient control program should pass through the determination of the diversity, prevalence, and pathogenicity of those parasites. This study aimed to determine the prevalence of intestinal parasites in dogs and cats and proceed to infection comparisons between young and adult animals. The detection of parasites in fecal samples was determined using flotation and immunofluorescent methods across 320 dogs and 64 cats from the Kvarner region in Croatia. The prevalence was calculated for each detected parasite in its host. Differences in prevalence between young animals and adults were analyzed. Parasites were detected in 32 dogs and 34.4% of cats. In total, 12 different genera were detected; Giardia spp. was the most prevalent parasite in both species, infecting 24.7% and 18.8% of investigated dogs and cats, respectively. Cryptosporidium spp. and Toxocara cati had a prevalence of (18.4%) and (6.3%), respectively. Prevalences of Giardia spp., Cryptosporidium spp., and Cystoisospora spp. were significantly (P < 0.05) higher in puppies compared to adult dogs. Pentatrichomonas hominis (P. hominis) was detected in one puppy. In addition to the first report of P. hominis, a relatively high prevalence of intestinal parasites in dogs and cats in the Kvarner region of Croatia was recorded, posing a potential zoonotic risk.