This article provides an explanation for previously observed gender differences in scientific performance during doctoral studies and the early career. Data is based on doctoral students in science, technology, and medicine at a Swedish university. We collected information on each doctoral student’s publication and employment history. We also created publication histories for the doctoral candidates main supervisors. The data was supplemented with information on gender, age, and research area. Informed by theories on academic socialization, our research questions focus on how gender differences in productivity during doctoral studies and the early career relate to research collaboration and behaviour/characteristics of the main supervisor. Results show that the gender gap in productivity during doctoral studies, and the early career, can be explained by the degree to which the doctoral students co-author publications with their main supervisors and the size of their collaborative networks.