The Nipah virus (NiV) is one of the most lethal viruses which can infect humans and lead to fatal encephalitis. The recent significant awareness of NiV is due to its elevated death rate and effective transmission capabilities among humans. With its recurrent outbreaks and exceptionally high mortality rate, the NiV infections have emerged as one of the most concerning hazards to public health. The exploration of NiV and its characteristics revealed that NiV has two distinct strains, namely, the Malaysia (NiVM) strain and the Bangladesh (NiVB) strain. In this paper, we propose a novel Caputo fractional order mathematical model to simulate the dynamics of the two strains NiV. The positivity and boundedness of the model’s solutions are investigated. The existence and asymptotic stability of the equilibrium points of the model are examined. The analysis of basic reproduction number is presented to determine whether the infection will die out or persist. The effects of key parameters of the model on its dynamical behaviors are also explored. Finally, efficient numerical technique is used to confirm the analytical results through detailed numerical simulations.