A third-order numerical model based on one-dimensional computational fluid dynamics is developed for kinetic Stirling engines. Various loss mechanisms in Stirling engines, including gas spring hysteresis loss, shuttle loss, appendix displacer gap loss, gas leakage loss, finite speed loss, piston friction loss, pressure drop loss, heat conduction loss, mechanical loss and imperfect heat transfer, are considered and embedded into the basic control equations. The non-equilibrium thermal model is adopted for the regenerator to capture the oscillating features of the gas and solid temperatures. To improve the numerical stability and accuracy, the implicit second-order time difference scheme and the second-order upwind scheme are adopted for discretizing the time differential terms and convective terms, respectively. Experimental validations are then conducted on a beta-type Stirling engine with the extensive experimental data for diverse working conditions. The results show that the developed model has better accuracies than the previous second-order models. Good agreements are achieved for predicting various critical system parameters, including pressure-volume diagram, indicated power, brake power, indicated efficiency, brake efficiency and mechanical efficiency. In particular, both the experiments and simulations show that the Stirling engine charged with helium tends to have much lower optimal working frequencies and poorer performances compared to the hydrogen system. Based on the analyses of the losses, it reveals that the pressure drop in the flow channels plays a critical role in shaping the different behaviors. The pressure drop in the helium system is much larger and more sensitive to the frequency increase due to the much larger viscosity of gaseous helium. Hydrogen is a superior working gas for a Stirling engine. The transient characteristics of the oscillating flow and the associated thermal interactions between gas and solid in the regenerator are finally analyzed in order to have an insight of the complex thermodynamic process. The study provides a promising numerical approach in simulating Stirling engines for further understandings of their operating characteristics and the underling mechanisms.