Extra-short implants, of which clinical outcomes remain controversial, are becoming a potential option rather than long implants with bone augmentation in atrophic partially or totally edentulous jaws. The aim of this study was to compare the clinical outcomes and complications between extra-short implants (≤ 6 mm) and longer implants (≥ 8 mm), with and without bone augmentation procedures. Electronic (via PubMed, Web of Science, EMBASE, Cochrane Library) and manual searches were performed for articles published prior to November 2020. Only randomized controlled trials (RCTs) comparing extra-short implants and longer implants in the same study reporting survival rate with an observation period at least 1 year were selected. Data extraction and methodological quality (AMSTAR-2) was assessed by 2 authors independently. A quantitative meta-analysis was performed to compare the survival rate, marginal bone loss (MBL), biological and prosthesis complication rate. Risk of bias was assessed with the Cochrane risk of bias tool 2 and the quality of evidence was determined with the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. 21 RCTs were included, among which two were prior registered and 14 adhered to the CONSORT statement. No significant difference was found in the survival rate between extra-short and longer implant at 1- and 3-years follow-up (RR: 1.002, CI 0.981 to 1.024, P = 0.856 at 1 year; RR: 0.996, CI 0.968 to 1.025, P  = 0.772 at 3 years, moderate quality), while longer implants had significantly higher survival rate than extra-short implants (RR: 0.970, CI 0.944 to 0.997, P < 0.05) at 5 years. Interestingly, no significant difference was observed when bone augmentations were performed at 5 years (RR: 0.977, CI 0.945 to 1.010, P = 0.171 for reconstructed bone; RR: 0.955, CI 0.912 to 0.999, P < 0.05 for native bone). Both the MBL (from implant placement) (WMD: - 0.22, CI - 0.277 to - 0.164, P < 0.01, low quality) and biological complications rate (RR: 0.321, CI 0.243 to 0.422, P < 0.01, moderate quality) preferred extra-short implants. However, there was no significant difference in terms of MBL (from prosthesis restoration) (WMD: 0.016, CI - 0.036 to 0.068, P = 0.555, moderate quality) or prosthesis complications rate (RR: 1.308, CI 0.893 to 1.915, P = 0.168, moderate quality). The placement of extra-short implants could be an acceptable alternative to longer implants in atrophic posterior arch. Further high-quality RCTs with a long follow-up period are required to corroborate the present outcomes.Registration number The review protocol was registered with PROSPERO (CRD42020155342).