After 1802, James Hoban concentrated on his successful business partnership with Pierce Purcell in Washington, distancing himself from the politics and the lower pay of public improvement projects. Except for the White House, few of Hoban's buildings still stand. He also superintended the Capitol, completing the North Wing by 1800, when the seat of government moved to Washington.

Hoban became the superintendent of all Washington's public works in 1798. He directed the construction of the Treasury and War Department buildings, based on the design of English architect George Hadfield. Hoban and William Lovering provided modifications, and Leonard Harbaugh was the contractor. Hoban rebuilt the executive office buildings that were destroyed in the 1814 fire, with design changes. In 1818, he designed two additional government buildings facing Pennsylvania Avenue north of the two original department buildings. State to the east and War to the west (the old War Department site was used for the new Navy Department).

Hoban also designed the brick Georgian "Great Hotel" for Samuel Blodget Jr., a native of New Hampshire and an amateur architect, who invested heavily in the real estate of the national capital. Blodget offered the hotel as the first prize in a lottery scheme to boost property sales. Before 1810, it was the largest privately owned building in Washington, D.C. Hoban may have been the architect of the original church for Saint Patrick's parish on the corner of 10th and F Streets, N.W., and of stately Oak Hill, a fine residence President James Monroe commissioned for his retirement in Loudoun County, Virginia. Only Oak Hill still stands.