Bycatch is the most significant threat to marine mammals globally. There are increasing requirements for national governments to fulfil their obligations to international agreements and treaties to assess fisheries catch and bycatch of non-target species. Questionnaire surveys represent one low-cost method to collect data to estimate fisheries catch and bycatch of vulnerable species including marine mammals. Questionnaire surveys can be particularly advantageous when bycatch is being investigated on large spatial and temporal scales, or in data-poor areas. This review aims to provide the necessary guidance required to design and conduct questionnaire studies investigating marine mammal bycatch. To do so, a systematic review was conducted of the methods used in 91 peer-reviewed or grey literature questionnaire studies from 1990 to 2023 investigating marine mammal bycatch. Literature was searched, screened, and analysed following the RepOrting standards for Systematic Evidence Syntheses (ROSES) protocols. A narrative synthesis and critical evaluation of the methods used were conducted and best practice recommendations are proposed. The recommendations include suggestions for how to generate representative samples, the steps that should be followed when designing a questionnaire instrument, how to collect reliable data, how to reduce under-reporting and interviewer bias, and how weighting or model-based bycatch estimation techniques can be used to reduce sampling bias. The review’s guidance and best practice recommendations provide much-needed resources to develop and employ questionnaire studies that produce robust bycatch estimates for marine mammal populations where they are currently missing. Recommendations can be used by scientists and decision-makers across the globe. Whilst the focus of this review is on using questionnaires to investigate marine mammal bycatch, the information and recommendations will also be useful for those investigating bycatch of any other non-target species.