The combination of enamel matrix derivative (EMD) with an autogenous bone graft in periodontal regeneration has been proposed to improve clinical outcomes, especially in case of deep non-contained periodontal defects, with variable results. The aim of the present systematic review and meta-analysis was to assess the efficacy of EMD in combination with autogenous bone graft compared with the use of EMD alone for the regeneration of periodontal intrabony defects. A literature search in PubMed and in the Cochrane Central Register of Controlled Trials was carried out on February 2019 using an ad-hoc search string created by two independent and calibrated reviewers. All randomized controlled trials (RCTs) comparing a combination of EMD and autogenous bone graft with EMD alone for the treatment of periodontal intrabony defects were included. Studies involving other graft materials were excluded. The requested follow-up was at least 6 months. There was no restriction on age or number of patients. Standard difference in means between test and control groups as well as relative forest plots were calculated for clinical attachment level gain (CALgain), probing depth reduction (PDred), and gingival recession increase (RECinc). Three RCTs reporting on 79 patients and 98 intrabony defects were selected for the analysis. Statistical heterogeneity was detected as significantly high in the analysis of PDred and RECinc (I2 = 85.28%, p = 0.001; I2 = 73.95%, p = 0.022, respectively), but not in the analysis of CALgain (I2 = 59.30%, p = 0.086). Standard difference in means (SDM) for CALgain between test and control groups amounted to −0.34 mm (95% CI −0.77 to 0.09; p = 0.12). SDM for PDred amounted to −0.43 mm (95% CI −0.86 to 0.01; p = 0.06). SDM for RECinc amounted to 0.12 mm (95% CI −0.30 to 0.55. p = 0.57). Within their limits, the obtained results indicate that the combination of enamel matrix derivative and autogenous bone graft may result in non-significant additional clinical improvements in terms of CALgain, PDred, and RECinc compared with those obtained with EMD alone. Several factors, including the surgical protocol used (e.g. supracrestal soft tissue preservation techniques) could have masked the potential additional benefit of the combined approach. Further well-designed randomized controlled trials, with well-defined selection criteria and operative protocols, are needed to draw more definite conclusions.