Unselective use of antibiotics to treat children with COVID-19 is one of the major issues during the pandemic in Serbia. Thus far, there has been no evidence about the predictors of multiple antibiotic use in the treatment of children with COVID-19. The purpose of this study was to assess the prevalence of antibiotic use, as well as to examine demographic and clinical factors associated with a greater number of antibiotics and with a longer antibiotic treatment administered to hospitalized children with COVID-19 during the lockdown in Serbia. This study included all children who were hospitalized from 6 March to 31 May 2020 at the only pediatric COVID-19 hospital, and who were confirmed to have SARS-CoV-2 infection. Demographic, clinical, and laboratory data were collected from medical records. The antibiotic treatment included the use of azithromycin, cephalosporin (ceftriaxone), ampicillin-amikacin, and hydroxychloroquine. The overall prevalence of antibiotics use in children hospitalized with COVID-19 regardless of age was 47.2% (43.3% in children aged 1–5 years and 44.4% in those aged 5–17 years). In children aged 1–5 years, not having a family member affected by COVID-19 (B = −1.38, 95% confidence interval [CI] −2.43, −0.34, p = 0.011), having pneumonia on chest X-ray (B = 0.81, 95%CI 0.34, 1.29, p = 0.002), being a boy (B = −0.65, 95%CI −1.17, −0.13, p = 0.018), and having higher C-reactive protein (CRP) values on admission (B = 0.12, 95%CI 0.07, 0.17, p = 0.001) were associated with the administration of a higher number of antibiotics. These factors, along with having fever (B = 3.20, 95%CI 1.03, 5.37, p = 0.006), were associated with a longer duration of antibiotic treatment in children aged 1–5 years. In children aged 5–17 years, having pharyngeal erythema (B = 1.37, 95%CI 0.61, 2.13, p = 0.001), fever (B = 0.43, 95%CI 0.07, 0.79, p = 0.018), and pneumonia on chest X-ray (B = 0.91, 95%CI 0.53, 1.29, p = 0.001), not having rhinorrhea (B = −1.27, 95%CI −2.47, −0.08, p = 0.037), being a girl (B = 0.52, 95%CI 0.08, 0.97, p = 0.021), and having higher CRP values on admission (B = 0.04, 95%CI 0.01, 0.06, p = 0.006) were associated with the administration of a higher number of antibiotics. These factors, not including the absence of rhinorrhea, were associated with a longer duration of antibiotics treatment in children aged 5–17 years. Demographic, epidemiological, clinical, and laboratory parameters were associated with the use of multiple antibiotics and a longer duration of antibiotic treatment both among children aged 1–5 years and those aged 5–17 years.