Introduction Monitoring the progress of fracture healing is essential in order to establish the appropriate timing that ensures adequate bone strength for weight-bearing. In the present experimental study on a rat model of femoral fracture healing, the measurement of bone density and strength by peripheral quantitative computerized tomography (pQCT) was correlated with the modal damping factor (MDF) method. Methods Four groups of 12 male six-month-old Wistar rats each were anesthetized and submitted to baseline femoral pQCT and MDF scanning, followed by aseptic midshaft osteotomy of the right femur which was fixed by a locking intramedullary nail technique. The animals were left to recover and re-scanned following euthanasia of each group after six, eight, 10, and 12 weeks, respectively. The parameters measured by the pQCT method were total bone mineral density (BMD) and polar strength strain index (SSIp). Results Fracture healing progressed over time and at 12 weeks post-osteotomy there was no statistically significant difference between the osteotomized right and the control left femurs regarding MDF, BMD, and SSIp measurements. The highest correlations for the osteotomized femurs were observed between MDF and BMD (r = -0.647, P = 0.043), and between MDF and SSIp (r = -0.350, P = 0.321), at 10 weeks postoperatively. The high to moderate correlations between MDF and BMD, and between MDF and SSIp respectively, support the validity of MDF in assessing fracture healing. Conclusions Based on our findings in this fracture healing animal model, the results from the MDF method are reliable and correlate highly with the total BMD and moderately with the SSI polar values obtained by the pQCT method of bone quality measurement. Further studies are needed which may additionally support that the MDF method can be an attractive portable alternative to monitor fracture healing in the community.