The “FLexible EPIdemic MOdeling Pipeline” (flepiMop) is an open-source software pipeline written in R and Python designed for creating and simulating wide range of compartmental models of infectious disease transmission and inferring parameters. A no-code configuration file is used to define the disease transmission and observation models, to allow models of varying complexity to be specified, from simple problems described by SIR-style models to more complicated models. The pipeline can also be used to simulate the dynamics of any infection that can be expressed as a compartmental epidemic model (including applications in within-host dynamics, etc.). flepiMop source is code is available on GitHub with link to detailed documentation on installation, specifying models, running simulations, etc. flepiMop is available for Windows WSL, MacOS, and Linux with a provided Docker image and an Anaconda environment.