The John Joseph Moakley United States Courthouse serves as headquarters for the United States Court of Appeals for the First Circuit and the United States District Court for the District of Massachusetts. The building houses two courtrooms for the Court of Appeals and 25 courtrooms for the District Court. In April 2001, the Courthouse was dedicated to honor Congressman John Joseph Moakley, dean of the Massachusetts Congressional Delegation and life-long public servant.

The attractive HarborWalk at the Moakley Federal Courthouse wraps around the west edge of Fan Pier, providing a stunning panoramic view of Boston Harbor from Downtown to East Boston. Along the HarborWalk, interpretive panels and ship silhouettes present the history of Fan Pier and Boston Harbor. A large medallion next to the HarborWalk shows the history of Boston Harbor and the Islands. This is a popular location with school groups doing stone rubbings. Picnic tables and benches allow visitors to enjoy the Harbor views. Restrooms for the general public are located next to the ground floor restaurant and are accessible directly from the HarborWalk. Plaques identify native plantings at the site.

Visitors to the courthouse can arrange to take an hour-long tour highlighting the art and architecture of the courthouse. Visitors may also view the specially commissioned permanent works by noted artist Ellsworth Kelly, as well as temporary exhibits on the ground floor and second floor of the Courthouse. The law library on the top floor is also open to the general public.

For those that would like to purchase food, The Daily Catch, a popular seafood restaurant on the ground floor next to the water transportation ramp, and the second-floor cafe looking out onto the Harbor, provide a variety of options. Inside the Daily Catch restaurant are two monitor screens donated by the Coca Cola Foundation to the Island Alliance providing a "virtual tour" of Boston’s Harbor Islands. During the summer, there is boat transportation to Little Brewster Island from the boat dock. Tall Ships and educational vessels often dock at the Courthouse. A ramp rider provides those with disabilities access to water transportation.