Coronavirus disease 2019 (COVID-19) restrictions have been correlated with vitamin D deficiency in children, but some uncertainties remain. We retrospectively studied vitamin 25-(OH) D blood levels in 2182 Italian children/adolescents hospitalized for various chronic diseases in the year before (n = 1052) and after (n = 1130) the nationwide lockdown. The type of underlying disease, gender, and mean age (91 ± 55 and 91 ± 61 months, respectively) of patients included in the two periods were comparable. Although mean levels were the same (p = 0.24), deficiency status affected a significantly higher number of subjects during the lockdown period than in the pre-COVID period (p = 0.03), particularly in summer (p = 0.02), and there was also a smoothing of seasonal variations in vitamin D levels. Particularly at risk were males (OR = 1.22; p = 0.03), the 1–5 year age group (OR = 1.57; p < 0.01) and the 6–12 year age group (OR = 1.30; p = 0.04). Infants appeared not to be affected (p = 1.00). In the post-COVID period, the risk of vitamin D deficiency was unchanged in disease-specific groups. However, the proportion of deficiency or severe deficiency differed significantly in the subgroup with endocrinopathy (higher; Chi-square p = 0.04), and with respiratory problems and obesity (lower; Chi-square p = 0.01 and p < 0.01, respectively). Conflicting/opposite literature results advocate for further studies to clearly indicate the need for supplementation during possible future periods of confinement.