Abstract Aim The aim of this study was to investigate the effects of a self‐assembling peptide ( SAP ) nanofibre hydrogel on healing of surgical periodontal defects in rats. Materials and Methods In vitro interactions between rat periodontal ligament ( PDL ) cells and SAP hydrogel (2.5% RADA 16) were assessed by cell proliferation assays. In vivo, maxillary first molars of 45 Wistar rats were extracted and after healing, bilateral periodontal defects were surgically created mesially in second molars. Defects were treated with RADA 16, Matrigel, or left unfilled. After 2 and 4 weeks, defect healing was evaluated by microcomputed tomography, histological and immunohistochemical analyses. Results Periodontal ligament cells grown on RADA 16 showed an gradual increase in proliferation up to 72 h. At 4 weeks post surgery, the bone volume fraction and trabecular thickness of defect areas in the RADA 16 group were significantly greater than those in other groups. Histologically, enhanced new bone formation was observed in the RADA 16 group. At 4 weeks, PDL ‐like collagen bundles ran oblique to the root surface in the RADA 16 group. Expression levels of PCNA ‐positive cells, vascular endothelial growth factor and osteopontin in the RADA 16 group were significantly greater than those in other groups. Conclusions Within the limitations of the study, application of the SAP hydrogel promoted healing of surgical periodontal defects by enhancing cell recruitment and possibly angiogenesis.