Due to its physical and chemical properties, hydrogen is an attractive fuel for internal combustion engines, providing grounds for studies on hydrogen engines. It is common practice to use a mathematical model for basic engine design and an essential part of this is the simulation of the combustion cycle, which is the subject of the work presented here. One of the most widely used models for describing combustion in gasoline and diesel engines is the Wiebe model. However, for cases of hydrogen combustion in DI engines, which are characterized by mixture stratification and in some cases significant incomplete combustion, practically no data can be found in the literature on the application of the Wiebe model. Based on Wiebe’s formulas, a mathematical model of hydrogen combustion has been developed. The model allows making computations for both DI and PFI hydrogen engines. The parameters of the Wiebe model were assessed for three different engines in a total of 26 operating modes. The modified base model considers the significant incompleteness of hydrogen combustion, which occurs at high air/fuel equivalence ratio. For PFI and DI hydrogen engines, equations and numerical values for the Wiebe model coefficients were determined to describe the dynamic and duration of combustion. Based on our simulation results we suggest using the sum of two Wiebe curves to describe combustion in zones with a lean mixture in DI engines. This allows a more accurate characterization of the combustion dynamics and pressure curves. In order to model a double hydrogen injection, we suggest using the sum of three Wiebe curves representing the combustion of the first injection in the flame front, the diffusion combustion of the second injection, and the relatively slow combustion in lean mixture zones. In the paper, we present a method for selecting the coefficients of each of the Wiebe curves.