In children, coronavirus disease 2019 (COVID-19) starts as a minor illness compared to adults, but during the ongoing COVID-19 pandemic, distinct SARS-CoV-2 variants and subvariants have changed options for therapies in both adults and children, especially for those with comorbidities such as allergies. On 25 April 2022, Remdesivir (RDV), a viral RNA-dependent RNA polymerase inhibitor, was approved by the Food and Drug Administration (FDA) for the treatment of pediatric patients 28 days and older, weighing ≥3 kg, hospitalized or non-hospitalized, who are at high risk of progression to severe forms of COVID-19. While RDV has been shown to have favorable effects in numerous types of research conducted on adults, such as shortening hospital stays, and has shown it has antiviral effects on various RNA viruses, there is a lack of findings regarding safety, tolerability, and efficacy of RDV in allergic pediatric patients since its initial FDA approval. This study aims to assess RDV’s efficacy and tolerability in treating pediatric patients with mild and severe forms of COVID-19-associated allergies such as asthma, allergic rhinitis, and atopic dermatitis and how RDV affects the duration of hospitalization, especially for these comorbidities. The most recent pandemic wave among children rose due to the high transmissibility of the Omicron variant, and this study analyzed changes between July 2020 and September 2022 at the National Institute of Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania. Our retrospective study included 250 children <18 years old, 42 (16.8%) had allergies, 132 were males (52.8%), age group 0–5 years old (80%), with a positive viral test for SARS-CoV-2. Severity was categorized as mild (43.6%), moderate (53.2%), and severe (1.6%) COVID-19, and treatment with RDV was administered in 50.4% (126/250) of children included in the study. The presence of comorbidities, asthma (7.2%), allergic rhinitis (4.4%), and atopic dermatitis (4.4%), was associated with an increased risk of developing severe COVID-19 infection in children,p< 0.05. We did not register deaths and severe complications; all cases evolved favorably under the instituted treatment. Laboratory abnormalities in transaminase levels 53.97% (ALT) and 61.9% (AST) were grades 1 or 2 and did not require discontinuation of the antiviral treatment,p< 0.05. RDV in children reduced the duration and evolution of COVID-19 and decreased the length of hospitalization in group-associated allergies;p< 0.05. This article summarizes RDV’s efficacy among children with COVID-19 and allergies when the clinical result was improved and reports positive effects on tolerability and reduced duration of hospitalization, especially in children with asthma, atopic dermatitis, and allergic rhinitis. More studies are needed to confirm our findings.