A rail mounting system is provided for mounting skylights and other structures directly to rib elevations of a metal panel roofing system. The rail mounting system has a side rail for each side of a skylight or run of skylights that mount to the metal panel roof's rib elevations. Each side rail includes a vertical riser wall, an upper flange extending from the riser wall to provide a top bearing surface for one side of a skylight or run of skylights, and a bottom shoulder structure extending from the riser portion which is adapted for attachment to a rib elevation of the roofing system. The rib elevations on which the side rails of the rail mounting system are attached provide structural support for the skylight or run of skylights supported thereon for substantially the entire length of the skylights or run of skylights.