During his consecration, Roman Emperor Theodosius II was staying at Chalcedon. His eunuch Chrysaphius attempted to extort a present of gold to the Emperor but as he was unsuccessful, he began to plot against the new Archbishop by supporting the archamandrite Eutyches in his dispute with Flavian.
St. Flavian presided at a council of forty bishops at Constantinople on November 8 448, to resolve a dispute between the metropolitan bishop of Sardis and two bishops of his province. Eusebius, bishop of Dorylaeum, presented his indictment against Eutyches. The speech of Flavian remains, concluding with this appeal to the bishop of Dorylaeum: "Let your reverence condescend to visit him and argue with him about the true faith, and if he shall be found in very truth to err, then he shall be called to our holy assembly, and shall answer for himself." Eventually the synod deposed Eutyches.
However, as Eutyches protested against this verdict and received the support of Dioscorus I of Alexandria, the Emperor convoked another Council to Ephesus. At this council, which assembled on August 8, 449, Eutyches and Dioscuros violently attacked the archbishop. The council reinstated Eutyches and Flavian died shortly afterwards, on August 11, 449, Flavian died at Hypaepa in Lydia, Asia Minor from the injuries he received from this attack and was buried obscurely.
After Theodosius II died in 450, his sister Pulcheria returned to power, marrying the officer Marcian, who become Emperor. The new Imperial couple had Flavian's remains brought to Constantinople in a way that, in the words of a chronicler, more resembled "a triumph .. than a funeral procession". The Council of Chalcedon, called in 451, condemned Eutyches, confirmed Pope Leo's Tome and canonized Flavian as a martyr.