During the last 40 years, problem- and project-based learning (PBL) has been widely adopted in engineering education because of its expected effectiveness in developing students’ professional knowledge and transferable skills. With a growing number of PBL researches and practices in engineering education, systematic or meta-analysis reviews were conducted regarding the definitions, history and development of PBL, and benefits for student learning outcomes. However, challenges in PBL implementation was little addressed in the current review works, and even less attention has been paid on how these challenges in implementation are related to the diverse PBL practices. This paper reviewed 108 research articles to explore the levels at which the currently reported PBL practice is being implemented, and what challenges in PBL practices are being addressed. This research illustrates the variety of PBL implementation at the course level, cross-course level, curriculum level, and project level. Across these four levels, similar challenges are reported at the individual level for teachers and students, as well as at the institutional level and the culture level. Recommendations on future research directions for engineering educational researchers and suggestions for engineering faculty and staff are proposed to optimise PBL curriculum design and inform future PBL implementation.