Ordained priest at Würzburg in 1786, he spent his entire life in that city, first as professor of Oriental languages and theology, then as rector of its Seminary, and finally as auxiliary bishop with the titular see of Hippos in partibus infidelium. Elected Bishop of Speyer, he died before taking possession of his cathedral.
Though in his youth he had inclined toward rationalism, later he corrected his errors and took his place among the most decisive apologists of the Church and its rights, both in the theological and philosophical spheres as well as in the political. Zirkel lived indeed in the turbulent era of the French Revolution and of Napoleonic conquests, and he worked tirelessly for the defence of Catholicism. A trusted counsellor of the hereditary prince Louis and of Queen Charlotte, he contributed to the downfall of the minister Count Maximilian von Montgelas, who had reformed Bavarian legislation in a liberal sense and proclaimed the equality of all religions before the State. A promoter of a Catholic league, an eloquent orator and a vigorous writer, he played a major part in the stipulation of the Concordat of 1817 between Bavaria and the Apostolic See. He wrote a Geschichte des Patronatsrechtes (1806) and a volume on Die deutsche katholische Kirche (1817). Surviving works include exegetical writings and printed sermons, as well as numerous articles.