Objectives: Within programmatic assessment, the ambition is to simultaneously optimise the feedback and the decision-making function of assessment. In this approach, individual assessments are intended to be low stakes. In practice, however, learners often perceive assessments designed to be low stakes as high stakes. In this study, we explored how learners perceive assessment stakes within programmatic assessment and which factors influence these perceptions. Methods: Twenty-six learners were interviewed from three different countries and five different programmes, ranging from undergraduate to postgraduate medical education. The interviews explored learners’ experience with and perception of assessment stakes. An open and qualitative approach to data gathering and analyses inspired by the constructivist grounded theory approach was used to analyse the data and reveal underlying mechanisms influencing learners’ perceptions. Results: Learners’ sense of control emerged from the analysis as key for understanding learners’ perception of assessment stakes. Several design factors of the assessment programme provided or hindered learners’ opportunities to exercise control over the assessment experience, mainly the opportunities to influence assessment outcomes, to collect evidence and to improve. Teacher–learner relationships that were characterised by learners’ autonomy and in which learners feel safe were important for learners’ believed ability to exercise control and to use assessment to support their learning. Conclusions: Knowledge of the factors that influence the perception of assessment stakes can help design effective assessment programmes in which assessment supports learning. Learners’ opportunities for agency, a supportive programme structure and the role of the teacher are particularly powerful mechanisms to stimulate the learning value of programmatic assessment.