Flow experience is related to well-being. Still, the question arises as to whether the flow is beneficial because of its intensity and frequency, or its contribution to well-being depends on the domain in which it is experienced. It was hypothesized that flow experienced in a domain that is perceived important and useful (i.e., the academic domain) contributes more to students’ well-being than flow experienced in domains that are perceived as less important and less useful (leisure and routine activities) even though it is in academic domain experienced less often and less intensely. This hypothesis was tested in two separate studies. In the first study, the flow was operationalized as a trait and the frequency of flow was measured via questionnaires. In the second study, the flow was operationalized as a state and the intensity of flow was measured via the experience sampling method. The samples were comprised of university students from Zagreb, Croatia. Both studies showed that flow in a domain that is perceived as more important and useful (i.e., the academic domain), although is experienced less often and less strongly, is more related to students’ well-being than flow in domains perceived by students as less important and less useful (leisure and routine activities). It was also tested if the association between academic flow and well-being is mediated by academic achievement. This hypothesis was not accepted. The results of this study indicate that it is important for students to have opportunities to experience flow in their studies because it is a pleasant state, related to better achievement, and it adds to their overall well-being.