Walking from origins to transit stops, transferring between transit lines and walking from transit stops to destinations—all add to the burden of transit travel, sometimes to a very large degree. Transfers in particular can be stressful and/or time-consuming for travellers, discouraging transit use. As such, transit facilities that reduce the burdens of walking, waiting and transferring can substantially increase transit system efficacy and use. In this paper, we argue that transit planning research on transit stops and stations, and transit planning practice frequently lack a clear conceptual framework relating transit waits and transfers with what we know about travel behaviour. Therefore, we draw on the concepts of transfer penalties and value of time in the travel behaviour/economics literature to develop a framework that situates transfer penalties within the total travel generalized costs of a transit trip. For example, value of time is important in relating actual time of waiting and walking to the perceived time of travel. We also draw on research to classify factors most important to users’ perspectives and travel behaviour—transfer costs, time scheduling and five transfer facility attributes: (1) access, (2) connection and reliability, (3) information, (4) amenities, and (5) security and safety. Using this framework, we seek to explicitly relate improvements of transfer stops/stations with components of transfer penalties and changes in travel behaviour (through a reduction in transfer penalties). We conclude that the employment of such a framework can help practitioners better apply the most effective improvements to transit stops and transfer facilities.