The use of cooperative learning in STEM disciplines has been linked to increased student achievement and performance. Faculty at two Midwestern Land-grant Universities collaboratively developed the Advanced Animal Systems Management course. The course was designed to facilitate interaction among students at both institutions through shared course lectures/discussions, cooperative peer review of work, and a joint field experience. The objective of this study was to determine students’ perceptions of trans-institutional cooperative learning on meeting the overall course goals and desired learning outcomes. Pre- and post-questionnaires were developed and administered during the first and last week of class to 11 students at Institution 1 and 9 students at Institution 2 (100% response rate). Student enthusiasm was high, with all students agreeing that they were interested in the course content area. Most students felt that the collaboration would be beneficial to the learning experience. At the end of the semester, most students did not think that the trans-institutional cooperative learning increased their understanding of course materials or helped their learning of concepts and principles. Additional learning activities are needed in future course offerings to foster more engagement and interaction of students.