The most common cause of severe diarrhea in children under five is rotavirus infection. Pediatric comorbidities are integral components that may affect the prognostic outcomes of rotavirus gastroenteritis (RVGE). However, little is known about RVGE severity in the presence of comorbid conditions in children under five years of age. This study aims to compare the clinical outcomes of rotavirus diarrhea in children with and without co-morbidities. Children under five years of age suffering from acute diarrhea and admitted to the Inpatient Department (IPD)/Intensive Care Unit (ICU) were included. ELISA was used to identify the rotavirus antigen in stool samples obtained from each of the study participants. The Vesikari severity score index was used to assess the degree of disease severity. Out of the 76 participants recruited, rotavirus was detected in 13 (17.1%) cases. Comorbidities were present in 42 (55.2%) of the study participants, and eight (10.5%) patients had RVGE. The most common comorbidities observed were severe acute malnutrition (SAM) followed by malignancies. An increased frequency of diarrhea, vomiting, and fever was observed among children under five years of age with rotavirus diarrhea (p < 0.05). A significant difference in the severity of clinical manifestations was observed among RVGE patients with comorbidities (p < 0.05). This study demonstrated that rotavirus diarrhea was still common in hospitalized children under five years old, even though rotavirus vaccination was added to the universal immunization program. The presence of comorbidities further accelerated the deterioration of clinical conditions among RVGE patients highlighting the need for additional measures to prevent rotavirus infection in children with comorbid conditions.