Background: Malnutrition remains a major public health concern, particularly in developing countries, where children under the age of five are most vulnerable.This study aims to assess the prevalence of malnutrition among children aged 6–59months attending Atbara Hospital from April to September 2024. Methods: A cross-sectional study was conducted at Atbara Hospital, River Nile State, Sudan. Data were collected from medical records of children diagnosed with moderate acute malnutrition (MAM) and severe acute malnutrition (SAM) based on mid-upper arm circumference (MUAC), weight-for-height z-scores, and the presence of bilateral oedema. Monthly trends were analyzed to determine fluctuations in malnutrition prevalence over the study period. Results: The findings indicate a significant increase in both MAM and SAM cases over the six-month period. MAM cases, identified using MUAC and weight-for-height z scores, rose steadily from 14 in April to 17 in September. Similarly, SAM cases, particularly those classified by MUAC <11.5 cm, increased from 1 in April to 44 in September. The prevalence of bilateral oedema remained low, with only a few cases reported throughout the study period. The increase in malnutrition cases was particularly pronounced during the rainy season, which is associated with higher rates of diarrheal diseases and food shortages. Additionally, the ongoing Sudanese conflict and the influx of internally displaced persons (IDPs) to the River Nile State have placed a significant burden on Atbara Hospital, leading to increased admissions of malnourished children. Conclusion: The study highlights a concerning rise in malnutrition cases among children under five, emphasizing the need for urgent public health interventions. Strengthening nutritional support programs, improving healthcare accessibility, and addressing the socio-economic factors contributing to malnutrition are essential to mitigating this growing crisis. Further research is needed to explore long-term solutions and the impact of conflict and displacement on child nutrition.