Follicular unit hair extraction (FUE) is effective for hair restoration but is less successful on scarred tissue due to reduced vascularity and altered tissue architecture. Stem cell therapy can enhance tissue regeneration, possibly improving FUE outcomes on scarred tissue. This study investigated the impact of stem cell therapy prior to FUE on scarred tissue. Sixty patients with scalp scars from trauma or previous surgeries were divided into two groups. Group A (n = 30) received autologous stem cell therapy followed by FUE, while Group B (n = 30) underwent FUE without prior stem cell treatment. Autologous stem cells were harvested from patients’ adipose tissue and injected into the scarred area four weeks before FUE. Outcomes were assessed at 3-, 6-, and 12-months post-transplantation, focusing on hair density, graft survival rate, and patient satisfaction. Histological examinations evaluated tissue regeneration. Group A showed significantly higher hair density (mean increase of 45%) and graft survival rates (87%) compared to Group B (mean increase of 25%, graft survival rate of 60%) at all follow-up points (P < 0.05). Histological analysis revealed enhanced neovascularization and reduced fibrosis in the stem cell-treated group, with 70% more new blood vessels and 50% less fibrotic tissue compared to the control group. Patient satisfaction scores were higher in Group A (average score of 8.5 out of 10) versus Group B (6.0), indicating better aesthetic outcomes and reduced scar visibility. Pre-treatment with autologous stem cell therapy significantly improved FUE effectiveness on scarred tissue, enhancing graft survival, hair density, and patient satisfaction. Further research is recommended to optimize this therapeutic strategy.