He made secondary studies in Bragança and at sixteen, he enrolled at the University of Coimbra, to study theology. Two years later he left to study law, that he concluded in 1873. Then he became secretary of the governor of Angra do Heroísmo, Azores, and later of Viana do castelo. In 1878, he was elected to the House of Representatives.

He married Filomena Augusta da Silva Neves on 10 February 1880, the couple had two children; Maria Isabel Guerra Junqueiro on 11 November 1880, second wife without issue of Luís Augusto de Sales Pinto da Mesquita de Carvalho (1868–1931) and Júlia Guerra Junqueiro in 1881, unmarried and without issue. He died in Lisbon at the age of 72.

In 1885 he published at Porto A velhice do Padre Eterno, that generated strong criticism from Portuguese Catholic Church. After the British Ultimatum and the political crisis associated, he was involved in the political debate in 1891, writing some best-sellers that had huge impact in public opinion, contributing to the discredit of the Portuguese monarchy and the success of the Portuguese Republican Party in the 1910 Portuguese Revolution. He translated into Portuguese short stories by Hans Christian Andersen.

In 1940 Junqueiro’s daughter donated his estate in Porto that became the Guerra Junqueiro Museum.