Introduction: Anorexia nervosa (AN) is a psychiatric disorder with a high mortality rate and significant prevalence in the paediatric population. Preliminary reports during the COVID-19 pandemic suggested an increased incidence of AN among children and adolescents. The objective of this study was to analyse new cases of AN before, during, and after the pandemic, with a particular focus on the physical manifestations of the disease. Methods: This single-centre, retrospective study included new AN cases from the hospital database of a regional paediatric hospital (a reference centre for AN) between 2013 and 2023. Data analysed included the duration of the disease, body mass index (BMI), weight loss, length of hospitalisation, laboratory markers (leukopenia, anaemia, hypoproteinaemia, hyperferritinaemia, hypophosphataemia, dyslipidaemia, and hypothyroxinaemia) and clinical features of malnutrition (such as amenorrhea bradycardia, pericardial effusion, and cortical/subcortical atrophy). Results: This study was conducted in a Polish regional hospital. We analysed 228 hospitalized female patients aged 10 to 18 years diagnosed with AN, focusing on clinical characteristics, biochemical markers, and the impact of the COVID-19 pandemic. The COVID-19 pandemic was shown to have a significant impact, with longer hospitalisations observed during and after the pandemic and a lower BMI on admission post-pandemic compared to pre-pandemic. In addition, nutritional treatment became more prevalent over time while biochemical markers such as anaemia, hypothyroidism, hypophosphataemia, and dyslipidaemia were statistically more common post-pandemic. Conclusions: This study demonstrates a significant impact of the COVID-19 pandemic on the clinical course and hospitalisation patterns of paediatric patients with AN. These findings suggest that the pandemic may have exacerbated disease severity and altered treatment approaches, emphasizing the need for enhanced clinical management and follow-up strategies for AN in the paediatric population during such health crises.