The co-infection of Human Immunodeficiency Virus (HIV) and Hepatitis B virus (HBV) poses a major threat to public health due to their combined negative impacts on health and increased risk of complications. A novel fractional mathematical model of the dynamics of co-infection between HBV and HIV for Taiwan is presented in this paper. Detailed analyses are conducted on the possible impact of HBV vaccination on the dynamics of HBV and HIV co-infection. The next-generation matrix technique is used to calculate the fundamental reproduction number $R_0$ = max$\{R_1, R_2\}$, where $R_1$ and $R_2$ are the reproduction numbers for HBV and HIV, respectively. The disease-free and endemic equilibria of the co-infection model are calculated. An extensive investigation is carried out to determine the local and global stability of the disease-free equilibrium point through Rough Hurtwiz criteria and the construction of Lyapunov function, respectively. We demonstrate that when $R_1 < 1 < R_2$, HBV infection is eradicated, but HIV remains prevalent. If $R_2 < 1 < R_1$, the opposite outcome occurs. The real data from 2000-2023 for Taiwan is used to fit the model. The fitting results show how effectively our model handles the data. In addition, numerical simulations are run for different scenarios to observe how the vaccine and fractional parameters changed the model state variables, as well as how the solutions behaved and how quickly they reached the model's equilibrium points. According to the model's numerical analysis, greater vaccination efforts against HBV have a positive effect on the propagation of co-infection.