Dental implant osseointegration exhibits high success rates; however, further improvements are still possible. In this context, new strategies for the delivery of osteogenic biomolecules have gained increasing attention. Synthetic DNA hydrogels mimic the extracellular matrix and exhibit intrinsic bioactive potential. Their degradation releases phosphate and adenine, promoting mineralization and osteoblastic activity. Furthermore, they can serve as platforms for the controlled release of biomolecules. This study evaluated the effect of implant functionalization with a DNA hydrogel on peri-implant bone repair in rats. Following approval by the Institutional Animal Care and Use Committee, ten female rats were allocated into two experimental groups (n = 5): conventional implants (CONV) and DNA hydrogel-functionalized implants (DNA). Animals were euthanized at 10 and 28 days, corresponding to the early and intermediate phases of bone healing. Calcein and alizarin were administered on days 14 and 24, respectively. The analyses included removal torque testing, RT-qPCR, histology (H&E), micro-computed tomography (micro-CT), and dynamic histomorphometry by confocal microscopy. After normality assessment using the Shapiro–Wilk test, data were analyzed by one-way ANOVA (p < 0.05). The results demonstrated higher removal torque values in the DNA group, corroborated by micro-CT findings. Increased gene expression of markers associated with bone mineralization was also observed and confirmed by histological and confocal microscopy analyses. Therefore, implant functionalization with DNA hydrogels appears to be a promising strategy for enhancing peri-implant bone repair while also providing a platform for the future delivery of anabolic or antiresorptive biomolecules.