The aim of this in vivo microcomputed tomographic (μCT) experiment was to assess in real time the efficacy of a combination of recombinant human bone morphogenetic protein-2 (rhBMP-2) and biphasic calcium phosphate (BCP), with and without resorbable collagen membrane (CM), in regeneration of standardized calvarial defects (SCDs) in rats. A total of 30 female Wistar albino rats (n = 10/group) with a mean age and weight of 7.5 months and 275 g, respectively, were used. With the rats under general anesthesia, the calvaria were exposed using full-thickness periosteal flaps and unilateral SCDs of 4.6 mm diameter were created on the left parietal bone. Defects were left untreated (control group) or randomly filled with either BCP soaked in rhBMP-2 and then covered with CM (BMP + BCP + CM group) or BCP soaked in rhBMP-2 alone (BMP + BCP group). In vivo μCT scans were done at baseline and 2, 4, 6, and 8 weeks. Newly formed bone (NFB) and remaining BCP particles were assessed for their volumes (NFBV, BCPV, respectively) and mineral densities (NFBMD, BCPMD, respectively). In vivo μCT results showed scanty amounts of new bone at the peripheries of the defect in the control group. In the other two groups, near complete defect closure was evident at 8 weeks. The mean NFBV after 8 weeks was 4.63 ± 0.96 mm3, 11.82 ± 1.17 mm3, and 13.85 ± 1.89 mm3 for the control, BMP + BCP + CM, and BMP + BCP groups, respectively. After 8 weeks, the mean NFBMD was 0.38 ± 0.03 g/mm3, 0.24 ± 0.07 g/mm3, and 0.35 ± 0.03 g/mm3 for the control, BMP + BCP + CM, and BMP + BCP groups, respectively. After 8 weeks, the mean BCPV and BCPMD values for the BMP + BCP + CM and BMP + BCP groups were 2.73 ± 0.65 mm3, 0.33 ± 0.08 g/mm3, 2.49 ± 0.71 mm3, and 0.28 ± 0.03 g/mm3, respectively. The present real-time in vivo μCT experiment demonstrated that BMP + BCP, either with or without CM, was effective in promoting bone regeneration within rat SCDs and enabled new bone formation starting as early as 2 weeks.