Background/Objectives: In Italy, the prevalence of celiac disease (CeD) among children exceeds 1.5% and has steadily increased with a linear trend over the past 25 years. The clinical presentation is heterogenous and a change in onset symptoms has been described in recent years. The aim of the study is to describe the pattern of clinical presentation of CeD during the last 12 years in a single Italian center. Methods: We retrospectively enrolled all children diagnosed with CeD at Bambino Gesù Children Hospital, Rome between 1 March 2011 and 22 June 2023. To investigate the changes in pattern of clinical presentation, we divided the patient population into three groups of approximately 4 years each (respectively: 49, 48 and 48 months). Patients who previously received a CeD diagnosis in other centers were excluded. Results: Overall, 4478 patients were diagnosed with CeD at our center. 1082 were excluded, leaving 3396 available for analysis. We divided the study cohort into three groups: group 1 (n = 909), group 2 (n = 1103), and group 3 (n = 1384). Diagnoses of CeD increased by 17.5%. The trend of the non-classic form shows a significative increase (p = 0.000064), showing a high prevalence of bloating and abdominal pain and a significant reduction in celiac crisis (p < 0.0001). Conclusions: Annual diagnoses of CeD increased during the study period, and the clinical presentation has changed in recent years, showing an increase in the non-classic form and a reduction in more severe forms of celiac crisis.