Influenza is a contagious respiratory illness and can lead to hospitalization and even death. Understanding how comorbidities affect the severity of influenza can help clinical management. The aim of this study is to offer more information about comorbidities that might be associated with the severity of influenza in children. We used a statewide network in Rhode Island, USA, to extract data for laboratory-confirmed influenza cases among children 19 years old or younger. We identified 1169 lab-confirmed influenza cases. The most common comorbidities were asthma (17.1%), neurodevelopmental disorders (10.3%), gastrointestinal disorders (7.6%), atopic dermatitis (7%), and endocrine and metabolic diseases (6.8%). Interestingly, 80.8% (63 out of 78) of children who had an influenza-related hospital admission had at least one comorbidity, and among hospitalized children with influenza, the most common comorbidities were neurological diseases (28.2%, 22/78), gastrointestinal disorders (25.6%, 20/78), endocrine and metabolic diseases (24.4%, 19/78), and neurodevelopmental disorders (23.1%, 18/78). Children with endocrine or metabolic diseases were 8.23 times more likely to be admitted to the hospital, and children with neurological disorders were 6.35 times more likely to be admitted (OR: 8.23, 95% CI: 4.42–15.32 and OR: 6.35, 95% CI: 3.60–11.24, respectively). In summary, we identified specific comorbidities associated with influenza hospitalization and length of hospital stay, and these groups should be prioritized for public health interventions.