This paper provides a conceptual elaboration of the role of Problem-based Learning (PBL) in the integration of social sciences and humanities (SSH) with science, technology, engineering, and mathematics (STEM), and an analysis of the challenges this brings about. SSH-STEM integration is an endeavor that is timely, relevant, and urgent given the insufficient answers that higher education provides to the challenges social science and (especially) humanity faces. PBL can be argued as a pedagogical model to naturally cater to this demand. Based on two cases of integrated study programs from Aalborg University, Denmark, we analyze and discuss challenges and potential pitfalls in integrating SSH and STEM. As a result, we pinpoint learnings that can serve as timely guides in future iterations of problem-based, inter- and transdisciplinary endeavors in higher education.