Hydrogen is expected to play a key role in achieving a carbon neutral energy system in the future. Therefore, modelling of hydrogen is becoming an increasingly integrated part of sector coupled energy system modelling tools. However, results from different models and scenarios show different needs for hydrogen infrastructure and deployment of electrolysers. There is therefore an urgent need for a transparent communication of the main modelling features and input data that can impact the results related to hydrogen production in national energy systems. In this paper, we propose a framework that can be applied when modelling hydrogen in sector coupled energy systems. The proposed framework is based on the outcomes of a comparative assessment of different scenarios, which are conducted using five state-of-the-art energy system modelling tools. We discuss discrepancies in scenario results and quantify specific impacts related to varying different modelling features, such as model type, spatial and temporal resolution, grid modelling, boundary conditions, as well as input data and assumptions. Overall, the proposed framework can serve as a guideline for documentation and modelling of hydrogen in sector coupled energy systems and aims to increase transparency both for energy system modellers, as well as for policy and decision-makers.