Depression in male and female are commonly associated with different prevalence, severity, and, in some cases, distinct syndromes or subtypes. However, only a small amount of research has been conducted to completely understand the underlying neuroanatomical mechanisms. The goal of the current study was to provide neural markers for specific depression therapies by demonstrating the differences in aberrant prefrontal activity between male and female depressed subjects during an emotional autobiographical memory test. The study included 127 young adults who were randomly assigned to one of two groups: male depression (62 participants) or female depression (65 participants). The average oxyhemoglobin levels in the dorsolateral prefrontal cortex throughout the emotional autobiographical memory task were assessed utilizing 53-channel functional near-infrared spectroscopy imaging equipment. The oxy-Hb activation in the left dorsolateral prefrontal cortex (lDLPFC) and right dorsolateral prefrontal cortex (rDLPFC) had no significant interaction between groups and emotional valences. A significant main effect was found between male and female, with female depression groups showing lower oxy-Hb activity in lDLPFC and rDLPFC than male depression groups. Male and female depression patients showed distinct brain activation in the DLPFC during an emotional autobiographical memory test, suggesting potential specific neurological indicators for varied somatic symptoms in male and female depression patients. These distinctions should be taken into account while creating preventive measures.