McGowen was the son of James McGowen, a boilermaker, and his wife Eliza Ditchfield, immigrants from Lancashire and was born at sea, on the "Western Bride", on the way to Melbourne. His father worked building in bridges, initially in Victoria, and later in New South Wales. After limited schooling he was apprenticed as a boiler maker in 1870. He became a member of the United Society of Boilermakers and Iron Shipbuilders of New South Wales on its establishment in 1873, he became secretary in 1874. He entered the railways department and in 1888 was elected president of the executive of Trades Hall committee. He worked hard and successfully to raise funds to build the Trades Hall at Sydney.
In 1891, the New South Wales Trades and Labour Council established the Labor Electoral League, which developed into Australian Labor Party, and McGowen stood for election to the New South Wales Legislative Assembly seat of Redfern and was one of 35 Labor candidates to win and the most experienced unionist. He held the seat continuously to 1917.
While the Australian Labor Party eventually became the most disciplined in the world, the first Labor parliamentarians were almost as independent as their fellow parliamentarians. McGowen was one of three to sign the "pledge" to abide by party discipline. As a result of his increasingly skillfulness as a parliamentarian and his relative seniority he became Labor's parliamentary leader in 1894. After the 1898 election George Reid's Protectionist Government was dependent on Labor to push through New South Wales' adoption of Federation. McGowen's support for Federation was critical to Labor maintaining its support for the adoption of measures to implement Federation, even though it remained opposed to the Constitution adopted, which it saw as biased in favour of business interests. McGowen stood for the Federal seat of South Sydney in 1901, but was narrowly defeated.
McGowen's honesty and judiciousness were reassuring the public and were a major factor in Labor's 1910 election win. While he was Premier from to 1913, he was not an effective director of the parliamentary party, which he left to his deputy, William Holman. As well as Premier, he was also Colonial Treasurer during most of 1911 and Colonial Secretary from December 1911, both important portfolios. In 1913, while Holman was in England, he attempted to settle a gas workers' strike by threatening to replace them with non-union labour. This alienated the party and Holman deposed him as leader on his return in June 1913. McGowen became Minister for Labour and Industry until January 1914.
In regards to social reform, the new state Labor government carried out an active policy of subsidising hospitals and dispensaries in order to bring about the realisation of universal health care system. However, opposition by doctors to state control forced the government to concentrate on financing new and existing institutions, such as nursing services for remote bush districts, while Friendly Societies were subsidised and membership encouraged. As a result of the state Labour government's efforts, improved low-cost medical services were made widely available throughout New South Wales. In addition, public works were expanded, and important educational reforms were enacted, together with reforms in electoral law, income tax, arbitration, and housing for workers.
Three of his sons served in World War I, including one killed at Gallipoli in 1915 and he was a strong supporter of Australia's involvement in the war. The 1916 Labor conference decided to oppose conscription. McGowen disagreed and was expelled along with most of the parliamentary party.
At the 1917 election he was defeated by the official Labor candidate William McKell, but, now Nationalist, Premier Holman appointed him to the then unelected Legislative Council in July 1917.
He died of heart disease in Petersham and was survived by his wife, five of their seven sons, and two daughters. His largely attended funeral was held at St. Paul's Church, Redfern, New South Wales on 8 April 1922, and he was then buried at Rookwood Cemetery.Policy speech 1910.