Membrane-based separation processes are increasingly recognized as effective purification systems for green hydrogen, produced through ammonia cracking technology. These processes are valued for their energy efficiency, operational simplicity, and selective capabilities, and they benefit significantly from simulation-based approaches. Such methodologies expedite the exploration and evaluation of various membrane materials and operational strategies, which are crucial for the rapid development and optimization of membrane systems. However, the application of these simulations is often limited due to restricted access to process simulations and compatibility issues with existing commercial software tools. Additionally, the absence of software capable of assessing material properties and calculating the economic impacts at different scales limits the integration of studies from the molecular to the plant level. To address these challenges, this study introduces pySembrane, an open-source Python-based simulation package designed to lower the barriers to entry for the development and analysis of membrane systems. PySembrane provides users with advanced tools for the analysis of membrane systems, including specialized functions for evaluating material properties and process economics. This study presents case studies that illustrate the use of pySembrane in the screening of membrane materials and the optimization of membrane-based separation processes for the purification of green hydrogen. It also presents a case study on the integration of the membrane-based separation process with other unit operations, such as compressors and catalytic reactors. These case studies demonstrate the effectiveness of pySembrane in advancing membrane materials and operational strategies for green hydrogen separation, highlighting its potential to enhance process efficiency and sustainability.