Transfer of learning (ToL) is the endpoint of simulation-based training (SBT). It is affected by numerous factors, which can be classified into 3 categories: learner characteristics, work environment, and training design. The first 2 have been identified to some extent in previous research. In this study, the aim was to identify the instructional design (ID) features affecting the ToL in SBT. This qualitative study was conducted in 2 phases. Phase 1 covers thematic analysis of comparative studies in the field of SBT. A systematic search was performed on 6 databases of Ovid MEDLINE, EMBASE, PsycINFO, CENTRAL, Scopus, and Web of Science, and the references of related systematic reviews were also checked. In phase 2, semi-structured interviews were conducted with key informants (instructors and learners) and analyzed using directed content analysis. The results of the 2 phases were combined, and finally ID features of SBT were identified and categorized. In the first phase, 121 comparative studies were reviewed and in the second phase, 17 key informants were interviewed. After combining the results of the phases, the ID features affecting the ToL in SBT were classified into 3 broad categories and 15 subcategories as follows: (1) presimulation: preparation, briefing, and teaching cognitive base; (2) underlying theories: deliberate practice, mastery learning, and proficiency-based training; (3) and methods and techniques: distributed practice, variability, increasing complexity, opportunity for practice, repetitive practice, active learning, feedback/debriefing, simulator type, and simulator fidelity. Although learning is transferred from the simulated setting to the clinical setting, this process is not automatic and straightforward. Numerous factors affect this transfer. The results of this research can be used in designing and evaluating the SBT programs.