For entrepreneurs who intend to exploit university-owned technologies, a cooperative relationship with the university is critical. This study aims to better understand this entrepreneur–university cooperation. A key factor influencing the quality of this cooperation is the fairness perception of the entrepreneur. However, little is known about how these fairness perceptions are formed in this context. Therefore, to increase insight in entrepreneur–university cooperation, this study explores the formation of fairness perceptions by entrepreneurs who cooperate with universities (in so-called university spin-offs). This study assesses how the rules these entrepreneurs employ to form fairness perceptions differ from fairness rules that have been established in previous studies on organizational justice. The results show that, in addition to established fairness rules, there are also fairness rules that are more specific to this entrepreneurial setting. These specific rules complement the established fairness rules to provide a more comprehensive understanding of the formation of fairness perceptions by entrepreneurs cooperating with a university. Moreover, this study explores to what extent different entrepreneurs form fairness perceptions differently and finds that both experience and relational capital of the entrepreneurs within the university are two key sources of heterogeneity. Overall, this study contributes to the literature by conceptualizing how entrepreneurs form fairness perceptions in cooperating with universities and how this extends established wisdom in organizational justice theory. Moreover, the rules identified in this study provide clues for entrepreneurs who wish to improve their collaboration with universities, and may also apply to the relationships between entrepreneurs and large corporations and between entrepreneurs and venture capitalists.