Microencapsulated rejuvenator has been attracted much attention for self-healing bitumen. The diffusion coefficient is one of the key parameters to estimate the feasibility of rejuvenator to age bitumen. The objective of this research was to evaluate diffusion behaviors of microencapsulated rejuvenator in aged bitumen by a FTIR-ATR method. Various microcapsule samples were mixed in bitumen to form thin films. The core material of microcapsules used as rejuvenator was diphenylsilane (DPS), its fairly specific absorption band at 843 cm−1 was selected as a marker band to calculate the diffusion coefficient (D). The microstructure parameters, including contents, mean size and mean shell thickness of microcapsules, were considered to understand the diffusion behaviors under different temperatures (20, 30, 40 and 50 °C) in bitumen. The results showed that a larger mean size of microcapsules did not greatly affect the D values under the same temperature. In contrast, a higher mean shell thickness decreased the D values because of the decrement of damage probability of microcapsules under the same content. With the same microcapsule sample in bitumen, the D values presented a trend of linear increase when the content of microcapsules was increased. All these results indicated that the microstructure affected the diffusion behaviors based on the concentration of released rejuvenator. A preliminary model of diffusion behaviors of microencapsulated rejuvenator in bitumen was given based on the Arrhenius equation considering the microstructure of microcapsules, the amount of released rejuvenator and the age degree of bitumen. This model may be a guide to the construction and application of self-healing bitumen using microcapsules.