Situated on both sides of the Le Sueur River, in south-central Minnesota, Saint Clair began as an Indian reservation and agency.

The first settlers in the area were Charles Mansefield and Ansen W. Callen, who settled along the east side of Rice Lake, south of Saint Clair, in 1854.

In 1855, the Winnebago Reservation and Agency was established, which led to the settlement of a number of government officials and employees of the agency. Among these were General J.E. Fletcher, the Indian agent, and W.J. Cullen, the superintendent of the Indian school, as well as Joshua Ady, J.L. Alexander, George Culver, Henry Foster, A.L. Foyles, Newell Houghton, Peter Manaige, Charles Mix, and Asa White. John Johnson came to the agency as a blacksmith in 1856, and Lucius Dyer and J.B. Hubell came in 1861.

In 1863, the Indian agency closed, and other white settlers came. A township was formed later that year and named McClellan for the Union General George B. McClellan. In 1865, the Minnesota Legislature changed the township's name to McPherson.

A townsite was platted by Aaron Hilton in August of 1865, which corresponded to the current boundaries of Saint Clair. He named the town Hilton, for himself. By that time, the village had about a dozen houses, three general stores, three wagon shops, two blacksmith shops, two boot and shoe shops, two saloons, a hotel, and a mill, owned by Aaron Hilton, that produced lumber and shingles.

Hilton was appointed postmaster, and the post office moved from the agency building to the Brown Brothers General Store, which had been opened by George and James Brown. In 1867, the former Indian agency was converted into a hotel. In 1869, Hilton sold the mill to Hegle and Reader, and Hegle soon sold his interest in the mill to Peter Pfaff. James Brown was appointed postmaster in 1869, and Henry Mohr took the job in 1871 when Brown moved to the new town of Mapleton, where his mercantile store was the first business.

Other early businesses were run by J.C. Cook, who was a shoemaker, Charles Young, who ran a variety store, and Mathias Jost, who started a mercantile store. Fred Gerlich and H.R. King were druggists, and Dr. Eaton and Dr. E.B. Haynes were the first doctors in the village.

A newspaper was started by J.H. Barlow in October of 1880. Known as The Messenger, it wasn't in publication long.

Until 1886, the post office was still designated as the Winnebago Agency, and there was some confusion in the mail between Winnebago Agency and Winnebago. In February of that year, it was changed to Hilton, but only a couple of months later it was changed to Saint Clair, in honor of General James St. Clair, a Scottish soldier, and prominent Whig. Saint Clair became the name of the village.

Until 1887, the town was served by two school districts, District #70 and District #73. In August of 1887, the districts were consolidated, and a new brick school building was constructed in 1888.

The McPherson Town Hall was built in 1898.

By 1895, Saint Clair had about two hundred people, a daily stage to Mankato, four churches, a grade school, a boot and dye store, two blacksmith shops, a carpet weaver, wagon maker, furniture store, harness shop, livery stable, meat market, and two mills, as well as a druggist, a physician, and three saloons.

Another newspaper, the St. Clair Star, was started by J.W. Ward in March of 1897, but it was in publication for only a few months.

Telephone service came to St. Clair in 1904 when the St. Clair Bellview Telephone Company was organized. S.S. Babcock was the president and Henry Thielman was the manager. The telephone company's switchboard was in the back of Thielman's store for ten years before being moved to the second floor of the bank building. The St. Clair State Bank was organized by Henry Thielman and several other people.

In December of 1907, Saint Clair was incorporated as a village.

The Duluth, St. Cloud, Glencoe and Mankato Railroad came through shortly after the village was incorporated. Given its long name, the railroad soon became known as the ABC Line. Despite its name and intent, the railroad's tracks were never laid between Saint Clair and Mankato, largely because of inter-railroad rivalry. The ABC Line sold out to the Chicago and Milwaukee Railroad, and became part of the Chicago, Milwaukee, St. Paul and Pacific Railroad system.

Saint Clair became a city in 1973 when the Minnesota Legislature made all villages and boroughs within the state cities. With a population of under a thousand, St. Clair has never been a large city but, except for a few minor decreases, its population has been steadily growing.

The main routes through the city are Minnesota State Highway 83 and County Highway 15. Mankato is about eleven miles northwest of St. Clair, while Eagle Lake is about seven miles north.

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