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Despite anti-Irish lobbying by English Catholic bishops and a British government agent, Moran had the strong support of Propaganda officials and the endorsement of Pope Leo XIII himself. He was appointed Archbishop of Sydney on 25 January 1884 and arrived on 8 September.

His settling in was disrupted on 1 May 1885 by a summons to Rome. He believed he would be offered the see of Dublin, but determined to urge Leo XIII to allow him to return to Sydney. On arrival he was informed that he was to be made a cardinal. Far from a consolation prize, this was both a confirmation of Moran's high personal standing in Rome and an affirmation of Leo's belief in the importance of the new worlds.

Moran was determined to have all Catholic children in schools staffed by religious Orders. By 1911 more than three-quarters of the Catholic children in Sydney of primary-school age were in his system, and he had laid the basis for a similar secondary system. He almost trebled the number of teaching brothers and more than trebled the number of nuns. He had authorized the expenditure of more than £1,250,000 on building churches, schools and institutions. On the twentieth anniversary of his arrival he noted that he had personally blessed eighty-eight foundation stones for churches or schools in the diocese. The largest single building project was the near-completion of St Mary's Cathedral. He had first finished the northern end, then built the central section including 'the Cardinal's Tower' by 1900, and was able to consecrate it all, debt free, in 1905. In his last years he decided to begin work on the southern part of the original plan, set a foundation stone in 1909, and in the second half of 1910 was speaking almost weekly in a tour of parishes to raise money.

In deliberately developing an active public role, Moran acted on the assumption that in colonial society leadership was needed. While his sermons remained, as in Ireland, 'so learned that he was hard to follow', he delivered brief, impromptu speeches at Church functions which, by the 1890s, had become the delight of Sydney journalists. In this role he became one of the best known public figures in Australasia. Increasingly in the 1890s he advocated Federation and in 1896 was invited to address the People's Federal Convention at Bathurst. Next year he agreed to stand for election to the Australasian Federal Convention and, when sectarian feeling erupted, he persisted in his candidacy, believing that the civil rights of Catholics were at issue, but failed to win a position in the New South Wales delegation of ten. In the 1900s he continued to strongly advocate an independent defence and foreign policy, repeating earlier calls for a separate Australian navy and supporting schemes for military training programmes.

His increasing public support for the trade union movement, for the new Labor Party, and for what he called 'Australian socialism' alarmed conservative Catholics in Australia and overseas. In 1890 he had supported the trade union cause in the maritime strike, a year before the appearance of the papal encyclical Rerum novarum, for which he tried to provide Australian relevance in his 1891 public lecture, 'The rights and duties of labour'. At first cautious, by 1900 he had criticized many aspects of the industrial system, and on one occasion even quoted Karl Marx on the social consequences of capitalism. To some extent, his support for the Labor Party was influenced by his belief, expressed publicly in 1901, that Labor was 'the only party above religious prejudice'. By 1902 he was being criticized by other bishops for putting social reform ahead of their demands for 'educational justice'. In 1905 he upset both Prime Minister (Sir) George Reid and the leading Catholic editor J. Tighe Ryan by denying that the Labor Party's platform made it unacceptable to Catholics. The great enemy of Australia, he said, was 'not socialism … but imperial jingoism'. In his last year, he both intervened in State politics to persuade a Catholic not to abandon support for the tottering McGowen Labor government and provoked worried letters from American Catholic bishops, including Cardinal Gibbons, because of his strong public support for the 1911 'socialist' referenda proposals.