A self-aligning stuffing box having a spherical joint between the upper and lower portions of the housing permits universal movement of the upper portion relative to the lower portion to permit a rod to pass through the bore if the axis of the rod is misaligned relative to the axis of the bore in each of the upper and lower housing portions. An energized seal in the upper housing resides at or below the spherical joint due to a downwardly depending central portion of the upper housing which extends into a recess formed in the lower housing permitting the height of the stuffing box to be relatively short. A second seal is positioned above the first seal and may be spaced sufficiently above the first seal to permit a flapper valve to be installed between the seals. The flapper valve is mounted through a port in the upper housing which is accessible without disassembly of the stuffing box, the seals or the wellhead.