The United Arab Emirates (UAE) and Qatar are similar in many aspects, including social structure, political life, and religious identity. However, there exists a considerable difference in their foreign policies toward one of the most important regional non-state actors, the Muslim Brotherhood. Since its independence in 1971, Qatar has developed strong relations with the Muslim Brotherhood organization. On the other hand, some of the Gulf countries, including the UAE, Saudi Arabia, and Bahrain, have remained skeptical toward having good relations with the movement. Particularly, after the Arab revolutions of 2011, the Emirati leadership pursued an anti-Muslim Brotherhood policy together with other regional allies. During this period, Qatar was under severe criticism as a consequence of its support for the Muslim Brotherhood movement. This distinction might be observed comprehensively in practice, yet it has not been adequately examined in a historical and ideological context. There is a lack of studies on the core determinants of Qatar and the UAE’s policy toward the Muslim Brotherhood. In light of this gap in literature, this work seeks to clarify why these two countries have such diverging policies toward the movement. Therefore, this study focuses on how the policies of Qatar and the UAE toward the Muslim Brotherhood diverged significantly, particularly in the past two decades.