Pterygoid implant placement has not been a common treatment modality to manage the atrophic posterior maxilla. This randomized, controlled clinical trial evaluated the accuracy of dynamic navigation using trace registration (TR) technology in pterygoid implant placement when compared to free-hand surgery. Partially edentulous patients requiring at least one pterygoid implant to rehabilitate the atrophic posterior maxilla were included. Implant accuracy (in a prosthetically directed context) and the relation of the placed implants to the greater palatine canal (GPC) were evaluated using EvaluNav to compare the preoperative CBCT plan with the postoperative CBCT implant location. Osseointegration success, mucosal thickness, implant length, time spent for surgical placement, and ease of prosthetic restorability via degree of multi-unit abutment angulation were assessed. A total of 63 pterygoid implants were placed (31 using TR, 32 using free-hand) in 39 partially edentulous patients. Mean deviations between the planned and actual position for TR-placed implants were 0.66 mm at the coronal level, 1.13 mm at the apical level, 0.67 mm in depth, and 2.64 degrees of angular deviation, compared to 1.54 mm, 2.73 mm, 1.17 mm, and 12.49 degrees, respectively, for free-hand implants. In relation to the GPC, TR implants were more accurate when compared to the presurgical plan and took less surgical time. The mean mucosal thickness measured for all implants was 5.41 mm. Most implants were 15 to 18 mm long, and most prostheses (92%) could be accommodated by a 17- or 30-degree multi-unit screw-retained abutment. TR implants had greater short-term osseointegration success rates than free-hand implants (100% vs 93.75%). Pterygoid implant surgery can be a predictable and successful modality for prosthetically directed implant rehabilitation in the atrophic posterior maxilla, is more accurate than free-hand surgery, and takes less time when using dynamic navigation via TR.