A matsayinsa na Ministan tsaro, kuma shugaban kwamandoji na Egyptian Armed Forces, Sisi ya shiga cikin juyin mulkin da aka tunbuke Morsi daga shugabanci a ranar 3 ga watan Yuni, shekarar, 2013, don mayar da martani a kan zanga-zangar Misra a watan Yuni shekara ta, 2013, wanda ya kira a matsayin juyin gwamnati daga 'yan cikinta. Ya rushe Kundin Dokar Misra na shekarar 2012, sannan ya sabunta, tare da wasu manyan 'yan adawa da malaman addini, wata sabuwar dokar gudanar da siyasar ƙasar, wadda ya hada da yin zaɓe game da sabon kundin ƙasar, da zaɓen 'yan majalisa da gwamnoni. An maye Morsi da shugaba Adly Mansour, wanda ya zabi sabbin kabinet. Gwamnatin ta afkawa Muslim Brotherhood da mabiyansu a watan da ya biyo baya, sannan kuma da wasu yan'adawa a kan tunbuke gwamnatin Morsi. A ranar 14 ga watan Augusta, shekarar, 2013, yan'sanda sun gudanar da August 2013 Kisan Rabaa, da kashe da ruruwan fararen hula da jikkata dubbai, wanda ya janyo suka daga kasashen duniya.[7]
A ranar 26 ga watan Maris, shekarar, 2014, don amsa wa masu son ya nemi shugabancin kasar, sai Sisi ya yi ritaya daga aikin soji, kuma ya bayyana cewar zai yi takarar shugabancin kasar a shekarar, 2014.[8] Zaben, ya gudana daga ranar 26 zuwa ranar 28 ga watan Mayu, da Dan hamayya daya, Hamdeen Sabahi,[9] inda aka samu kashi arba'in da bakwai daga cikin dari (47%) na masu kada kuri'u, wanda Sisi ya yi nasara da fiye da kashi 97% na kuri'un da aka kada.[9][10][11] An rantsar da Sisi amatsayin Shugaban kasan Misra a ranar 8 ga watan Yuni, shekarar, 2014. Gwamnatin Sisi ta baiwa hukumar sojin Misra karfin da bata bincike,[12] hakan yasa wasu jaridu suka kira shi da dictator kuma mai karfa-karfa, da danganta shi da tsoffin dictators din kasar.[12][13]
↑cite news |url=http://search.ebscohost.com/login.aspx?direct=true&db=pwh&AN=89930743&site=pov-live |title=The Anonymous Dictator |last=Giglio |first=Mike |date=16 August 2013 |work=Newsweek Global |access-date=25 July 2015 |last2=Dickey |first2=Christopher |issue=29 |volume=161 |issn=0028-9604 |last3=Atef |first3=Maged |last4=Jones |first4=Sophia |author-link2=Christopher Dickey |via=EBSCOhost |url-access=subscription |quote=That Egypt has a new strongman is no longer in doubt. Since the Egyptian military ousted the democratically elected President Mohamed Morsi last month following protests across the country, posters of Egypt's de facto leader, Gen. Abdel Fattah al-Sisi, have become more ubiquitous on Cairo streets than Sphinx souvenirs. The head of the Army stares out from café walls and the windows of government buildings, the red and the gold of his uniform remaining bright, even as the features of his face fade under the relentless sun. "He is the one we can trust," read some of the posters. Others call him "the eagle of the Arabs."