Australia’s fisheries research agencies all conduct stock assessments of varying complexities to assess the status of key fish stocks. However, the modelling approaches taken, data analyses that underpins the stock assessments and the level of peer review that is undertaken are variable (Dichmont et al. 2018, Haddon et al. 2018). The Status of Australian Fish Stocks (SAFS; Flood et al. 2016) program has aimed to make the reporting of these assessments consistent among jurisdictions. Additionally, in recognition of the data limited nature of many of the species being assessed in SAFS there has also been work undertaken to train jurisdictional stock assessment staff in data limited stock assessment techniques (Haddon et al. 2019). However, while there are a substantial amount of modelling tools available, most jurisdictions have stock assessment scientists that are model users rather than developers. Consequently, there is a need to provide guidance on how to use these appropriately so as to strengthen the quality of the outputs of the models. Developing guidance (defined as help and advice about how to do something or about how to deal with problems) is important and a set of stock assessment guidelines that describes each method currently used in Australia, outlines the method, required biological and fishery data, levels of uncertainty, and pros and cons is an important facet to demonstrating best practice in management of Australia’s fisheries. The guidance will provide transparency in the modelling process and has the potential to remove or moderate controversy regarding modelling outputs and the resulting management implications. This guidance (hereafter guidelines) are not intended to be prescriptive but provide guidance on a suite of methods from full-blown bioeconomic models and integrated assessments (e.g., SS3) through to data-poor approaches such as catchMSY.