This study evaluates the influence of early healing on clinical and radiological outcomes of guided tissue regeneration (GTR) procedures of vertical intrabony defects in patients with aggressive periodontitis (AgP) in a 12-month follow-up. The influence of patient-related, site-specific and technical aspects on optimal early wound healing was also assessed. This analysis included 25 patients with 61 intrabony defects. All sites were treated according to guidelines of minimally invasive surgical technique with the use of bone grafts and collagen membranes. Early post-operative healing was evaluated using the Early Wound-Healing Index (EHI). Changes in clinical and radiological parameters were assessed 12 months postoperatively. After 2 weeks, primary healing (EHI ≤3) was observed in 44 sites (72.13%) and secondary healing was present in 17 sites (22.87%) (EHI = 4). The presence of thin gingival phenotype was significantly associated with an increased risk of secondary healing (OR = 0.203; p = 0.014). At 12 months, GTR resulted in a significant clinical attachment level gain, as well as probing pocket depth reduction and radiographic defect depth reduction. Primary or secondary healing did not affect these outcomes. Thick gingival biotype might be a prerequisite for optimal early wound healing. However, the type of early healing seems not to affect the long-term outcomes after regenerative treatment in aggressive periodontitis patients.