Background <p>To determine the most appropriate fiducial markers distribution strategy in navigation surgery for three different tilted implant scenarios by comparing the target registration error (TRE) of tilted implants in fully edentulous maxillae.</p> Methods <p>The cone beam computed tomography scanned a maxillary edentulous model with 16 bone-anchored mini-screws (8 for registration and 8 for target registration error measurement), which was further imported into the navigation system for registration and target registration measurement. Each of the 5 strategies was performed six times, and the measurements were repeated twice around 4 target points each time. A mixed linear model was utilized for data analysis.</p> Results <p>Registration distribution, measurement site, and their interaction had a statistically significant influence on TREs (<i>P</i> = 0.010, 0.000, and 0.001, respectively). Two markers on the anterior alveolar crest, 2 in the buccal of the anterior alveolar ridge, and 2 on both sides of the maxillary tuberosity can realize the minimal TREs for tuberosity-pterygoid-palatine implant (TPP) at both coronal and apical points. No significant TRE differences were found for apical points of mesial tilted implant in ‘all on four’ and zygomatic implants among the 5 registration strategies.</p> Conclusions <p>For TPPs, incorporating fiducial markers on maxillary tuberosity for registration can help reduce the TRE in dynamic navigation.</p> Trial registration <p>Not applicable.</p>