Prendergast was one of the first Labor members of the Victorian Legislative Assembly, being elected for North Melbourne in 1894. In September 1897, Prendergast was arrested and charged with obstructing a footpath on Bourke Street, Melbourne, after he refused to move when instructed to by a police officer—the case was dismissed by the court. At the 1897 election, Prendergast was defeated by William Watt (another future Premier), but regained the seat in 1900, and held it until it was abolished in 1927. He then shifted to the electorate of Footscray, which he represented until his death. In all he was an MP for 40 years, but was noted more for his fiery stump oratory than any real ability: the historian Kate White calls him "mediocre."