Universities operate in an environment characterized by complexity, unpredictable challenges, rapid change and stakeholder demands. University employees are a key resource to achieve the strategic goals of the institution, linked to this complexity. Therefore, a conducive environment that fosters employee engagement in the university is critical. Employee engagement as a concept encompasses employees’ positive attitude towards the organization and its values, whereby employees continuously improve how they perform their work to improve organizational effectiveness. Organizational effectiveness is the ability of the organization to proactively adapt and adopt new ideas to continuously improve its operations. The purpose of the study was to explore the application of Systems Thinking as a strategic approach to foster employee engagement across functional boundaries in Universities of Technology. Employee engagement is central to achieving the strategic goals of Universities of Technology. To achieve the objectives of this study, a qualitative research methodology was used. The study was underpinned by a constructivism philosophical worldview. A total of 15 participants were purposively selected from the employees of two universities of technology. Semi-structured face- to-face interviews were used to collect data. Thematic Analysis was applied to analyze data. The findings revealed that Systems Thinking would create a conducive environment to foster Employee Engagement across functional boundaries in universities of technology. In addition, the findings revealed the prevalence of silo practices in the universities of technology. Without Systems Thinking in the institution, departments generally operate in silos and there is no institutionalized philosophy to foster employee engagement, collaboration and knowledge sharing within and beyond functional boundaries.