Bobcaygeon was incorporated as a village in 1876, and became known as the "Hub of the Kawarthas". Its recorded name bob-ca-je-wan-unk comes either from the Mississauga Ojibway word baabaagwaajiwanaang "at the very shallow currents", giishkaabikojiwanaang "at the cliffed cascades" or obaabikojiwanaang "at currented rocky narrows", or from the French beau bocage "beautiful hedged farmland". The first lock in the Trent-Severn Waterway was built in Bobcaygeon in 1833. The town is situated on three islands, along with the main land.
French explorer Samuel de Champlain, during his 1615 military expedition through the French colony of Canada in New France, passed through the area that would later become Bobcaygeon. In 1763, France ceded the colony to Great Britain, and it continued as the British colony of the Province of Quebec. In 1791, the colony was divided, with the area including the future Bobcaygeon becoming part of Upper Canada.
By the early 1830s, the colonial government of Upper Canada had completed its survey of the Township of Verulam and the area began to attract settlers. Thomas Need, who arrived in 1832, is recognized as one of the earliest settlers of the Township of Verulam and is the founder of Bobcaygeon. With his purchase of 3,000 acres (12 km2) of land, Need built a sawmill, gristmill, and the first store.
In 1833, the government began construction of a lock and canal at the narrows between Pigeon Lake and Sturgeon Lake. This was the first lock constructed on the Trent–Severn Waterway. The community began to develop around the lock, sawmill, and gristmill. Need became the first postmaster of the growing community.
The government had reserved and surveyed a townsite on the north bank of Bobcaygeon River between Sturgeon and Pigeon Lakes, which was named Rokeby by visiting Lieutenant Governor John Colborne. Need laid out streets and plotted lots on the island, which was named Bobcaygeon. Today, Bobcaygeon designates an area on both sides of the Bobcaygeon River, after the post office was established on the island by postmaster Need.
In 1841, the colony of Upper Canada merged into the new colony of the Province of Canada. In 1844, Need sold his profitable business interests to Mossom Boyd, and returned to England. In the 1850s, the economic development of Bobcaygeon was stimulated by Boyd's lumbering business, as he and his sons built up a logging enterprise that was recognized as the third-largest logging operation in Upper Canada. In addition to timbering, the Boyds also operated a system of steamboats under the name Trent Valley Navigation Company, as well as an experimental beefalo herd on Boyd Island. Descendants of this herd remain in Alberta.
With Canadian Confederation in 1867, Bobcaygeon became part of the province of Ontario in the new country of Canada. By 1869, Bobcaygeon was a village with a population of 800 in the Township of Verulam, Victoria County. There was a good trade-in lumber, limestone, hides, grain, and the GalKay lead mine. There were stagecoaches to the Ontario communities of Lindsay, Peterborough, and Minden. In summer, boats travelled to Lindsay and Peterborough. The average price of land was $20 per acre (equivalent to $532 in 2020).
Bobcaygeon, with a population of about 1,000, was incorporated as a village by a Victoria County by-law in 1876.
A group of local businessmen worked for many years to bring a railway into Bobcaygeon. Sir Sam Hughes sat on the board of the Lindsay, Pontypool & Bobcaygeon Railway. The line was leased to the Canadian Pacific Railway on completion. In July 1904 the first passenger train steamed into town. The service lasted until 1957, the railway lands becoming the Beach Park.The village government joined with the Township of Verulam in 1999. In 2000, it was amalgamated with the other municipalities of Victoria County by the provincial government following the recommendations of the Victoria County Restructuring Commission, led by commissioner Harry Kitchen. Now Bobcaygeon exists as a community within the City of Kawartha Lakes.