Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which when addressed will improve estimates of magnitudes, patterns, drivers and trace the potential origin of CH4 emissions. We identified the need (i) for both long‐term high frequency measurements of stem CH4 emissions to understand the fine scale processes, alongside rapid large‐scale measurements designed to understand variability across individuals, species and ecosystems; (ii) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (iii) to develop a mechanistic model including passive and active transport of CH4 from the soil‐tree‐atmosphere continuum. Addressing these challenges would help to constrain magnitudes and patterns of CH4 emissions, and would allow for the integration of pathways and mechanisms of CH4 production and emissions into process‐based models. These advances will facilitate upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local‐to‐global CH4 budget.