Patr. Meletius Pegas sent Cyril to Poland in 1596 to lead the opposition by the Orthodox to the [[Union of Brest]] that proposed a union of Kiev with Rome. During this time, he was a professor at the Orthodox academy in Vilnus, now the capital of Lithuania. In 1601, he was elected Patriarch of Alexandria, succeeding Patr. Meletius Pegas, a position he filled with dedication for nineteen years. During this time he re-organized the finances of the patriarchate and repaired churches in addition to preaching and maintaining constant correspondence with the Patriarch of Jerusalem and Cyprus.
In 1612, he was [[
locus tenens]] of the Church of Constantinople for a short time. On [[November 4]], 1620, the [[Holy Synod]] of Constantinople elected Cyril Patriarch of Constantinople. His patriarchate was broken into five different periods: 1620 to 1623, 1623 to 1633, 1633 to 1634, 1634 to 1635, and 1637 to 1638, by intrigues involving the the papacy, reformists, Jesuits, and the Ottoman sultan that included schemes against Cyril to discredit him by spreading rumors he was a Calvinist. After each [[deposition]], Patr. Cyril was re-elected by the [[clergy]] supported by the Orthodox population.
It is alleged that the great aim of his life was to reform the Church on [[Calvinism|Calvinistic]] lines, and to this end he sent many young Greek theologians to the universities of Switzerland, the northern Netherlands and England. In 1629, his famous ''Confessio'' (Calvinistic in doctrine) was published in Latin, but as far as possible accommodated to the language and creeds of the Orthodox Church. From 1629 to 1633, it appeared in two Latin editions, four French, one German and one English. The "Confession" started a controversy in the Eastern Church which culminated in 1672 in the convocation by [[Dositheus II of Jerusalem|Dositheus]], [[Patriarch of Jerusalem]], of a [[synod]] by which the Calvinistic doctrines were condemned. Since then, eminent historians, theologians, and researchers have attempted to clarify whether Cyril Lucaris was the actual author of the "Confession" attributed by the Calvinists to him. While Cyril denied it verbally a number of times and proclaimed his Orthodox faith in his letters as well by his attitude, he did not disavow the "Confession" in writing. The orthodoxy of Cyril Lucaris himself has continued to be a matter of debate in the Eastern Church. Even Dositheus, in view of the reputation of the great patriarch, thought it expedient to gloss over his [[heterodoxy]] in the interests of the Church.