Background: In 2014, the Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund) introduced a new funding model. Following notice of their 2014-2016 allocation, Morocco took the bold decision to reallocate its entire allocated investment (US$ 8 029 632) for health systems strengthening (HSS) and submitted a comprehensive request for funding solely for interventions to strengthen the health system. Aims: To explore the specific barriers and facilitators to Morocco's novel development and submission of a cross-cutting HSS funding request to the Global Fund and to document lessons learned and recommendations for policy and programme leaders interested in leveraging Global Fund investments for health systems. Methods: A thorough desk review of key documents and 15 in-depth qualitative interviews were conducted with key stakeholders in Morocco in 2017. Results: In preparation for the funding request, Morocco carried out a comprehensive assessment of the health system, which included extensive dialogue with stakeholders and partners. This action was critical to developing a shared understanding and support for adopting a cross-cutting HSS approach. Despite concerns about potential negative effects of diverting funding from disease-specific programmes, visionary leadership advocated effectively for investing in HSS, and this paved the way for the development of a clear Concept Note requesting Global Fund financial support for the health system more broadly. Conclusion: Morocco was the first country in the Global Fund's Middle/East North Africa region to invest its entire Global Fund allocation in strengthening the health system. Many important lessons have been learned from this novel experience and these are presented for shared learning. This opportunity for learning is timely as countries begin preparations for the upcoming funding cycle.