This paper describes applying a new brain-based instructional approach called "Tailored Instructions and Engineered Delivery using Protocols" (TIED UP) in an engineering classroom. Brain-based strategies leverage our knowledge about the functioning of the human brain to deliver the course information effectively. Although brain-based methods have been tested extensively in K-12 education, their application in STEM higher education has been scarce. This study demonstrates its effectiveness in teaching complicated engineering concepts such as mechanism synthesis and stress analysis. TIED UP adopts the brain-based instructional methodology to create a set of easy-to-follow protocols that any STEM instructor can adopt. The results show a significant improvement in the students' conceptual understanding compared to a control condition. The method may benefit the long-term retention of information learned in the class.