Endpoints that patients and clinicians consider important may differ based on patients' preferences and values. Several methods are available to elicit patient preferences in a succinct and methodologically valid manner. We conducted a scoping review of methods used to elicit patient preferences in invasive procedures to provide a framework for researchers and clinicians to incorporate these measures into future efforts. MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials and health and psychological instruments database were searched from inception until September 2020. Articles that examined patient preferences for any invasive procedure were eligible for inclusion. Selection and extraction were completed in duplicate. Preference elicitation methods were identified and summarized. Three hundred ninety-four articles (n = 76,921 patients) were included representing several surgical specialties. Of included studies, 11.7% (n = 46) used both quantitative and qualitative methods, 81.2% (n = 320) used quantitative methods only, and 7.1% (n = 28) used qualitative methods only to elicit preferences. The most frequently employed quantitative method to elicit preferences was simple choice selection, while one-on-one interviews with participants was the most frequently used qualitative method. Preference elicitation was the primary outcome in 74.6% (n = 294) of included studies. There are several methods to elicit patient preferences in surgical research. Qualitative methods are valuable for exploring views and generating consensus statements. Quantitative methods are better suited for assessing relative preferences, establishing preference thresholds, or ascertaining the presence of preferences. The choice of method should align with the specific research objectives.