Agarkar became associated with Lokmanya Tilak while studying in college. By then, they were both fired with the idea of serving their motherland. In 1881, Agarkar and Tilak together started the English newspaper Maratha and the Marathi newspaper Kesari, with Agarkar as the editor of Kesari. Later they also formed the Deccan Education Society and under its auspices started the Fergusson College in 1885. Agarkar started teaching in this college and later became the Principal of the College, holding the office until his death. He believed that social revolution should occur first, that all undesirable social practices like child marriages and untouchability should first be expelled before attaining political freedom. This led to differences between him and Lokmanya Tilak, who gave supreme priority to attaining freedom.
Unable to work together anymore under these differences, Agarkar resigned from the editorship of Kesari in October 1887 and started his own newspaper Sudharak (reformer) in 1888. He propagated individual freedom, rationalism and social justice through the medium of Sudharak. He also strongly voiced his opposition to unfair social practices like the Caste System (unequal treatment to people of lower castes), child marriage, making widows bald and Grantha-Dharma-Pramanya (blind following of religious scriptures and practices without present day context). Sudharak was published both in English as well as Marathi languages. Namdar Gopal Gokhale shouldered the responsibility of the English version of Sudharak for a brief period of time.
Agarkar was a staunch supporter of individualism. He also presented modern views about women’s dressing, before the society. He was a secular rationalist. He considered equality, consent and freedom to be important factors in the political and social context; that manmade social inequality should be kept to a bare minimum. He defined social progressiveness simply as having a system that provides reasonably equal comforts for all. He believed that intellectual debate is essential for social health. Agarkar expired unexpectedly, at the young age of thirty-nine years.