Undernutrition significantly compromises immune function, particularly in vulnerable populations. This study explores the impact of undernutrition on apoptotic pathways and thymocyte development in rats, shedding light on potential mechanisms underlying immune suppression. This study investigates the effects of undernutrition on apoptotic pathways and thymocyte development in rat models. Undernutrition was induced by competitive suckling, leading to weight deficits of 40% or more. Thymocytes were analyzed using flow cytometry to assess mitochondrial function, caspase activation, and subpopulation alterations among thymocytes, providing insights into the mechanisms underlying immune suppression due to undernutrition. The undernourished rats showed reduced thymus weight, modifications in thymocyte subpopulations, and diminished mitochondrial potential. The analysis of caspase activation unveiled a significant role of caspase 9 in early apoptosis, suggesting a link between mitochondrial dysfunction and the apoptosis of thymocytes induced by undernutrition. These alterations in thymic structure and apoptotic pathways align with previous studies, emphasizing the vulnerability of the thymus to undernutrition. The alterations observed in thymocyte subpopulations and caspase activation patterns provide insights into the intricate relationship between undernutrition, thymic function, and immune suppression. This study contributes to understanding how undernutrition during lactation affects thymic function and apoptotic pathways. These findings highlight the critical necessity for additional research to unravel the underlying mechanisms and identify potential therapeutic interventions to alleviate the detrimental impact of undernutrition on thymic development and immune function.