The European-American community was founded by David Hill, Isaiah Kelsey, and Richard Williams, who arrived in the Tualatin Valley in 1841, followed by six more pioneers in 1842. The locality went by two other names—East Tualatin Plains and Columbia—before it was named "Hillsborough" in February 1850 in honor of Hill, when he sold part of his land claim to the county. On February 5, 1850, commissioners chosen by the territorial legislature selected the community to be the seat of the county government. Hill was to be paid $200 for his land after plots had been sold for the town site, but he died before this occurred, and his widow Lucinda received the funds.
The town's name was later simplified to Hillsboro. A log cabin was built in 1853 to serve as the community's first school, which opened in October 1854. Riverboats provided transportation to Hillsboro as early as 1867 when the side-wheel steamer Yamhill worked on the Tualatin River.
A brick building was constructed in 1852 to house the county government, followed by a brick courthouse in 1873. In 1891, the courthouse was remodeled and a clock tower was added and the building was expanded with an annex in 1912. A new courthouse replaced the brick structure in 1928. The last major remodel of the 1928 structure occurred in 1972, when the Justice Services Building was built and incorporated into the existing building.
The city's first fire department was a hook and ladder company organized in 1880 by the board of trustees, (now city council). A drinking water and electricity distribution system added in 1892–93 gave the town three fire hydrants and minimal street lighting.
In 1871, the Oregon and California Railroad line was extended to the area, but it ran just south of town because the city did not want to give the railroad land in exchange for the rail connection. Hillsboro was incorporated as the Town of Hillsboro on October 19, 1876, by the Oregon Legislature. The first mayor was A. Luelling, who took office on December 8, 1876, and served a one-year term. Notable later mayors included Congressman Thomas H. Tongue (1882 and 1886) and state senator William D. Hare (1885).