Children suffering from severe acute malnutrition (SAM) have a weakened immune system. The relationship between malnutrition and alterations in the frequency of peripheral blood mononuclear cells (PBMCs) remains unclear. This study investigated the altered immune responses in Bangladeshi children with SAM compared to healthy children. PBMCs were collected from 24 healthy children and 25 children with SAM upon their hospital admission and after 21 days of nutritional therapy at a nutritional rehabilitation unit. Flow cytometry was employed to assess various subsets of T cells, B cells, and natural killer (NK) cells. Children with SAM exhibited significantly lower levels of activated (CD25+) B cells (SAM vs. healthy: 0.18 % vs. 0.30 %, p = 0.031) and NK cells (SAM vs. healthy: 4.9 % vs. 9.6 %, p = 0.003) compared to healthy controls. Similar immune responses were observed in SAM children during both hospitalization and discharge, with NK cell percentages showing slight increases but remaining significantly lower than in healthy children (SAM endline vs. healthy: 5.9 % vs. 9.6 %, p = 0.032). Notable reductions were also observed in CD62+ helper T cells, CD62L+ cytotoxic T cells, and CD62L+ B cells. These results suggest that although SAM children recover clinically, their immune systems remain compromised during discharge.