It was hypothesized that hyperbaric oxygen (HBO) could increase bone healing efficiency according to a protocol with a special window of healing time when maxillary sinus lateral augmentation is performed with only xenograft. The histomorphometric efficiency of HBO on the maxillary sinus lateral augmentation was examined by designing five different in vivo healing periods. Five patients receiving maxillary sinus lateral augmentation with xenograft each received a different treatment healing protocol: 6 weeks natural healing (control [Ctl]), 5 weeks with HBO (T1), 6 weeks with HBO (T2), 9 weeks with HBO (T3), and 13 months natural healing (TM). Biopsy samples were harvested, and quantitative histomorphometric analysis was performed regarding key factors BMP-2 and RUNX2. Analysis of variance and Tukey test were used for pairwise comparisons. Time-dependent relationships of the factors’ expression densities were conducted using quadratic regression fitting. There were statistically significant differences among the groups, except for T2/T3 and T2/TM for BMP-2 and for T2/T3 and TM/Ctl for RUNX2. Both BMP-2 and RUNX2 showed quadratic trends, presenting an initial upward trend and eventually a downward trend depending on T1, T2, and T3 groups. Early stimulation, achieved by keeping HBO until 6 to 9 weeks after maxillary sinus lateral augmentation with xenograft, seemed to be the time window that benefitted bone healing efficiency the most.