For much of its history, the Apostolic Episcopal Church has had a close relationship with Freemasonry. Its founder, Mar John Emmanuel, and many of its clergy have been Freemasons, as well as friends of the Church such as the Ecumenical Patriarch Athenagoras and Archbishop of Canterbury Geoffrey Francis Fisher, who was Grand Chaplain to the United Grand Lodge of England.

The association of Anglicanism with Freemasonry is very strongly established in nineteenth and twentieth-century history, despite significant opposition from some quarters in recent years. As a traditional Anglican church, the Apostolic Episcopal Church has not taken the path of some churches of outright rejection or prohibition of Freemasonry for its members, but has sought to promote a more nuanced approach appropriate for the present age. For the Apostolic Episcopal Church, the value of Freemasonry is principally as a repository of particular wisdom which provides a profitable school for moral self-improvement as well as an absorbing study in its own right. In addition, the AEC recognizes the contribution of Freemasonry to ecumenism and interreligious dialogue, and its capacity to unite people of disparate origins in a worthwhile common purpose.

Some say that Freemasonry is opposed to orthodox Christianity because it promotes a form of syncretism or otherwise conflicts with Christian beliefs and obligations. This assumes that Freemasons regard the beliefs and teachings of the Craft as if they were religious teachings requiring personal subscription and substituting for those of the Church. In practice, and after lengthy consideration of the issue, the AEC takes the view that Freemasonry does not require of its adherents the dogmatic beliefs that the Church imposes in order to assure the salvation of souls, nor does it, as some claim, teach a secret religion. What Freemasonry teaches is often expressed through symbol and allegory, and by being presented in ritual, invites the candidate to undertake a dramatised journey in search of enlightenment. Moreover, while much of mainstream Freemasonry is open to all without requirement of religious belief, and is essentially secular in nature, a number of branches specifically require the profession of the Christian faith and direct themselves to aspects of the Christian life.

In consequence, the fraternal and organizational aspects of Freemasonry are of incidental rather than principal interest to the AEC. That is not to deny the importance of charitable work nor of the social aspects of the Craft. The AEC has instead had much historically to do with those interesting teachings concerning both Christianity and esotericism that are now to be found in Rites and bodies that are outside that mainstream of Freemasonry. Indeed, those closely associated with the AEC, notably the late Mar Georgius of Glastonbury and the late Archbishop George Boyer, have in some cases been responsible for the preservation and rediscovery of aspects of Masonic tradition that would otherwise have been lost or forgotten. A number of the writings of Archbishop Boyer and other authorities continue to be carefully preserved in the AEC archives.

It is important to state in conclusion that while the AEC welcomes Freemasons as members without prejudice to their involvement in any aspect of the Craft, it is a Church and not a Masonic organization. Masonic membership is neither a requirement for joining the AEC, nor does it afford a person any privilege within our body.