Group work assessment is a challenging and complex practice for teachers. This study focuses on the challenges teachers perceive before and after participating in a group work assessment project that emphasizes individual assessment. By conducting a qualitative thematic analysis of twelve interviews with six teachers at upper secondary schools in Sweden, several challenges could be identified. The most prominent challenge concerning group work assessment is how to discern students’ individual performance within groups. This challenge has consequences for both the validity and the fairness of the assessment. Further, teachers experienced challenges with (un)fairness in group work assessment, in terms of both achieving fairness and having to deal with students’ emotions regarding perceived unfairness. The results also show how teachers perceive inadequate conditions, such as a lack of time and methods, and generate challenges in their practice, which is also related to reliability.