According to the United States Census Bureau, the city has a total area of 15.83 square miles (41.00 km), of which, 15.64 square miles (40.51 km) is land and 0.19 square miles (0.49 km) is water. It is located at latitude 43°45' north, longitude 87°44' west.

Sheboygan has a warm-summer humid continental climate typical of Wisconsin. In spite of its position on Lake Michigan there are vast temperature differences between seasons, although it is somewhat moderated compared with areas farther inland.

Before its settlement by European Americans, the Sheboygan area was home to Native Americans, including members of the Potawatomi, Chippewa, Ottawa, Winnebago, and Menominee tribes. In the Menominee language, the place is known as Sāpīwǣhekaneh, "at a hearing distance in the woods". The Menominee ceded this land to the United States in the 1831 Treaty of Washington. Following the treaty, the land became available for sale to American settlers. Migrants from New York, Michigan, and New England were among the first new Americans to settle this area in the 1830s, though the French had been present in the region since the 17th century and had intermarried with local people. One 19th century settler remarked: "Nearly all the settlers were from the New England states and New York." Lumbering was the first major industry, as trees were harvested and shipped to eastern markets through the Great Lakes.

Although Sheboygan was officially incorporated in 1846, much of the town had been platted in 1836, when property investors laid out more than one thousand lots.

By 1849, a wave of liberal, middle-class immigration triggered by the revolutions of 1848 had made the community known for its German population. As Major William Williams wrote on June 26, 1849: "Arrived at Sheboigin [sic] on the Wisconsin side, a small town, population purhaps [sic] from 700 to 1000. This is a promising place. There are a great many best class of Germans settling around it. 'Tis all along this Lake so far quite an interesting country." Between 1840 and 1890, Protestant Dutch immigrants also settled in the area, as did Irish refugees fleeing the Great Famine. A neighborhood in northwestern Sheboygan (between Martin Avenue and Alexander Court) was settled by Slovenian immigrants and acquired the name Laibach; it was also known as Vollrath's Division. According to a local Optimist member's account in 1963, in 1887 Sheboygan adopted a sundown town ordinance, banning African Americans from living there, though city leaders denied that any such ordinance was in effect.

In the spring of 1898, Sheboygan elected Fred C. Haack and August L. Mohr as aldermen, making them the first two Social Democratic Party candidates to be elected to public office in the United States. Haack had originally been elected in 1897 as a member of the Populist Party but joined the Social Democrats after they organized locally. Haack served as alderman for sixteen years before moving to Milwaukee and being elected as a Socialist alderman there. At the 1932 Socialist Party convention, Haack received recognition as the first Socialist officeholder in America.

In the early 20th century, many Orthodox Greeks, Catholic Slavs and Lithuanians immigrated to Sheboygan. In the late 20th century, Hmong refugees from Laos and Southeast Asia settled there.

Sheboygan has a mayor–council form of government. The full-time mayor is elected by general election for a term of four years, with no term limits and to an officially non-partisan position. The Common Council consists of ten alderpersons representing the city's ten aldermanic districts with a council president and vice-president presiding over them. A City Administrator oversees the day-to-day administration of the city and is appointed by the Common Council.

Sheboygan's 1916-built City Hall was remodeled throughout 2018 and into 2019, being re-dedicated on September 3, 2019, with a new north frontage becoming the building's new main entrance and making the building's vintage three-story staircase its most prominent feature within a new atrium.

The Sheboygan Police Department is the law enforcement agency in the city. Civil and criminal law cases are heard in the Sheboygan County Circuit Court, with municipal citations for Sheboygan and Kohler handled through the city's municipal court within the police headquarters building. The Sheboygan Fire Department provides fire suppression and emergency medical services, operating out of five fire stations throughout the city.

Sheboygan is represented in the Wisconsin State Assembly as part of both the 26th (Terry Katsma, R–Oostburg) and 27th (Tyler Vorpagel, R–Plymouth) districts, whose boundaries split the city along Geele Avenue from the west until North 18th Street, then Superior Avenue from North 18th Street to Lake Michigan. The city is also represented in the State Senate as part of the 9th district (Devin LeMahieu, R–Oostburg).

Sheboygan is in the 6th congressional district of Wisconsin, which is represented by Republican congressperson Glenn Grothman.

Interstate 43 is the primary north-south transportation route into Sheboygan, and forms the west boundary of the city. U.S. Route 141 was the primary north-south route into Sheboygan before Interstate 43 was built, and its former route is a major north-south route through the center of the city that is referred to as Calumet Drive coming into the city from the north, and South Business Drive/Sauk Trail Road from the south; between Superior and Georgia Avenues, the highway is known as 14th Street. Four-lane Highway 23 is the primary west route into the city, and leads into the city up to North 25th Street as a freeway. Other state highways in the city include Highway 42, Highway 28, which both run mostly along the former inner-city routing of U.S. 141. Secondary county highways include County Trunk Highway DL (CTH-DL) and the decommissioned CTH-LS to the north; CTH-J, CTH-O, CTH-PP, and CTH-EE to the west; and CTH-KK to the south.

For addressing purposes, the city's north-south zero point is Pennsylvania Avenue (increasing from 500 past that line in both directions), while west addressing zeroes out at the extreme eastern point of Superior Avenue at Lake Michigan (Sheboygan and Sheboygan County have no east addresses, and the little land existing northeast of that point stretches out the six '100 blocks' northward with xx50-xx90 numbers not otherwise used in most other addresses in Sheboygan).

Shoreline Metro provides public bus transit throughout the city, as well as in Kohler and Sheboygan Falls. All routes depart from the Metro Center, more commonly known as the "Transfer Point" located in the downtown.

Jefferson Lines and Indian Trails serve Sheboygan at the Metro Center, providing transportation to Milwaukee (and an Amtrak Thruway connection to the Milwaukee Intermodal Station) and Green Bay.

Historically the city was connected to Milwaukee, Chicago and Green Bay via the Milwaukee Interurban Lines, the Chicago & North Western Railroad and the Milwaukee Road. These railroads' passenger services were abandoned during the mid-20th century but in 2008 the Wisconsin Department of Transportation proposed to reestablish passenger service to Milwaukee and Green Bay via Fond du Lac and the cities along Lake Winnebago's west shore, though political complications in the 2010s have since mothballed rail expansion in Wisconsin.

Sheboygan is served by the county-owned non-commercial Sheboygan County Memorial Airport (KSBM) three miles northwest of the city.

Sheboygan is bounded on the east by Lake Michigan. The city has no active port in the 21st century. Blue Harbor Resort is located on a peninsula between the lake and the Sheboygan River's last bend. This site was formerly used as the headquarters of the C. Reiss Coal Company (now a Koch Industries division). It was their base of operations for ships to load and unload coal for delivery along the peninsula.

The Sheboygan River passes through the city, but dams in Sheboygan Falls prevent navigation upriver. Tall-masted boats are confined to the river downstream of the Pennsylvania Avenue bridge. Commercial charter fishing boats dock near the mouth of the river.

Two hospitals serve the city. Aurora Medical Center - Sheboygan County opened in July 2022 under Aurora Health Care. St. Nicholas Hospital operates as part of the Hospital Sisters Health System.