Background: Immunocompromised individuals, especially children with cancer, are at risk of acquiring cryptosporidiosis, which can result in severe morbidity and mortality. Aim: This work was conducted to evaluate the prevalence of Cryptosporidium parasite and its genotypes in children with cancer. Methods: Stool specimens were collected from 145 children in the Oncology unit of Pediatric Department, Zagazig University Hospital, Sharqiyah province, Egypt. Cryptosporidium infection was evaluated using modified Ziehl–Neelsen (MZN) staining and nested polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis. Results: The prevalence of Cryptosporidium infection in oncological children was 29.7% using microscopy and 25.5% using nested PCR. Genotypic characterization showed that 23 (62.2%) had C. hominis, 11 (29.7%) C. parvum, and 3 specimens (8.1%) were mixed infection of both genotypes. Cryptosporidiosis was significantly associated with diarrhea. However, no statistically significant difference was detected between the age, gender, residency, animal contact and malignancy type concerning to Cryptosporidium infection. Conclusion: This study concluded that Cryptosporidium is a prevailing opportunistic parasite among children with cancer. It should be considered in oncological patients especially those suffering from diarrhea which requires proper management to reduce its complications.