Studies show that teachers and students use humour when communicating with each other in a science education context. This study investigates the use of humour during a collaborative inquiry laboratory task on an undergraduate chemistry course and an undergraduate physics course. Seven groups of students working on a collaborative inquiry task were recorded on video. The videos were analysed utilising an analytical framework based on conversation analysis. During the tasks, humour was used in a dynamic way and the role of humour changed as the inquiry progressed. As expected, humour was used to create a group identity and to regulate negative emotions such as anxiety, frustration, uncertainty, boredom and disappointment. Humour also had an integral role in collaborative decision-making, for example in proposing and evaluating new ideas. Awareness of how humour can contribute to the regulation of emotions and collaborative decision-making might help students and teachers to better utilise humour in inquiry and learning.