Purpose: To conduct a comprehensive systematic review and meta-analysis on marginal bone loss (MBL) in dental implants, enhancing the understanding and management of both bone-level and tissue-level implants. Methods: MEDLINE-PubMed and Scopus databases were searched for relevant English articles (up to April 2024), assessing the MBL as the primary outcome. The relevant data were extracted, and a meta-analysis was performed to evaluate the effect of implant neck design. Results: A total of 17 studies were included for qualitative analysis. Out of the 21 articles included, 15 studies established a statistically significant difference in MBL between the study groups; however, the differences were not found to be clinically relevant. Bone-level implants with platform-switched abutments in most of the cases showed better marginal bone stability compared to tissue-level implants or bone-level implants with matching abutments. Seven RCT studies were evaluated for the MBL between bone-level and tissue-level implants. The difference in MBL between bone-level implants and tissue-level implants was statistically significant, with a greater loss of bone in bone-level implants (Mean Difference: 0.11, 95% CI:0.02 to 0.19, p = 0.01 and I² heterogeneity: 81%, p < 0.0001). Conclusions: This review underscores the need for standardized measurement techniques, consideration of patient-specific factors in clinical decision-making, and further long-term studies to optimize dental implant success and patient outcomes.