Injectable platelet-rich fibrin (i-PRF) has been used as an autografting material to enhance bone regeneration through intrinsic growth factors. However, fractionation protocols used to prepare i-PRF can be varied and the effects of different fractionation protocols are not known. In this study, we investigated the influence of different fractions of i-PRF on the physical and biological properties derived from variations in i-PRF fractionation preparation. The i-PRF samples, obtained from the blood samples of 10 donors, were used to harvest i-PRF and were fractioned into two types. The yellow i-PRF fractionation was harvested from the upper yellow zone, while the red i-PRF fractionation was collected from both the yellow and red zone of the buffy coat. The viscoelastic property measurements, including the clot formation time, α-angle, and maximum clot firmness, were performed by rotational thromboelastometry. The fibrin network was examined using a scanning electron microscope. Furthermore, the concentration of growth factors released, including VEGF, TGF-β1, and PDGF, were quantified using ELISA. A paired t-test with a 95% confidence interval was used. All three viscoelastic properties were statistically significantly higher in the yellow i-PRF compared to the red i-PRF. The scanning electron microscope reviewed more cellular components in the red i-PRF compared to the yellow i-PRF. In addition, the fibrin network of the yellow i-PRF showed a higher density than that in the red i-PRF. There was no statistically significant difference between the concentration of VEGF and TGF-β1. However, at Day 7 and Day 14 PDGF concentrations were statistically significantly higher in the red i-PRF compared to the yellow group. In conclusion, these results showed that the red i-PRF provided better biological properties through the release of growth factors. On the other hand, the yellow i-PRF had greater viscoelastic physical properties. Further investigations into the appropriate i-PRF fractionation for certain surgical procedures are therefore necessary to clarify the suitability for each fraction for different types of regenerative therapy.