The Market–Frankford Line begins at 69th Street Transportation Center, in Upper Darby.  From there it is elevated over Market Street until 46th Street, where it curves north and descends underground via a portal at 44th Street. At 42nd Street, the tunnel returns to the alignment of Market Street.

At 32nd Street, the tunnel carrying the Subway-Surface lines joins the MFL tunnel.  The MFL tracks are in the center and the trolley tracks are on the outside. 30th Street station consists of an island platform between the two innermost tracks for Market–Frankford Line trains, and outboard "wall" platforms for Subway–Surface route 10, 11, 13, 34, and 36 trolleys.  After passing beneath the Schuylkill River, the next stop to the east for Market–Frankford Line trains is at 15th Street; Subway-Surface trolleys also have stations at 22nd Street and 19th Street.  15th Street is the central interchange station for the MFL, Subway-Surface trolleys, and Broad Street Line.  The Subway-Surface tracks end in a loop beneath 13th Street at Market just after crossing above the Broad Street Line.

Though it now tunnels in a straight line directly beneath Philadelphia City Hall, prior to 1936, the original MFL trackage between 15th and 13th Street stations separated and looped around the foundation of City Hall (eastbound trains around the south side returning to be westbound trains from the north side).  Parts of that original alignment can still be seen from subway-surface cars as they pass south of City Hall en route to 13th Street station (as well as the bridgework in the ceiling of the southbound platform of the City Hall stop on the Broad Street line).  The Market Street tunnel continues east to Front Street and then turns north, where it rises in the median of I-95.  The rail line and freeway share an elevated embankment for about ½ mile (0.8 km), including Spring Garden station (which replaced Fairmount station on the Frankford Elevated).  The line then heads under the southbound lanes and over Front Street on an elevated structure that turns northeast onto Kensington Avenue, which merges with Frankford Avenue, which the line follows to its end.  Just north of Pratt Street, a curve to the north brings the line to its current terminus at the Frankford Transportation Center, which replaced the original Bridge-Pratt Sts. terminal.