The wharf was established in the 1850s, when workers and building materials began arriving to construct a military fort completed in 1859. After Alcatraz became a long-term military prison in 1868, the steamer General McPherson made twice-daily runs to the dock, ferrying officers, prisoners, and supplies between the island and the mainland. A narrow walkway called the Sally Port led from the dock up to the original citadel, elevated above a dry moat designed to slow any prisoner bold enough to make it this far.

During its years as a federal penitentiary, the wharf was the point of no return. At least one prisoner attempted escape by dressing as an officer and simply walking onto a departing boat. He failed. The cold, swift currents of San Francisco Bay and the watchful eyes of guards made the wharf as much a barrier as the walls of the cellhouse above. Today, that same dock welcomes tourists rather than convicts, though the chill of the bay waters remains unchanged.

The wharf has been repaired and rebuilt many times over its century and a half of service. Major seismic rehabilitation in the early 2000s reinforced the structure against the earthquakes that periodically remind San Francisco of its precarious geology. Building 64, the Alcatraz Defensive Barracks built in 1905, still stands at the dock's edge. The wharf now serves thousands of daily visitors who come to walk the corridors of a prison that held some of America's most dangerous criminals.