As of 1900 (interpreted from Form CT1000), the Pennsylvania Railroad -- which did not include "Lines West of Pittsburgh" -- was organized into Grand Divisions, Divisions, and Railroads. Railroads represented in bold are included in the listings but are believed to be independent railroads (many are confirmed so).
| Grand Division | Division | Railroad |
| United Railroads of New Jersey Division | New York Division | |
| Central R.R. of New Jersey | ||
| New York & Long Branch R.R. | ||
| Amboy Division | ||
| Belvidere Division | Belvidere Delaware R.R. | |
| West Jersey Railroad | ||
| Camden & Atlantic Railroad | ||
| West Jersey & Seashore R.R. | Cape May Division | |
| Atlantic City Division | ||
| Pennsylvania Railroad Division | Philadelphia Division | Schuylkill River Branch |
| Delawre Extension | ||
| Junction R.R. | ||
| Skuylkill Division | ||
| Frederick Division | Colombia & Port Deposit R.W. | |
| Middle Division | ||
| Lewistown Division | Sunbury & Lewistown R.W. | |
| Milroy Branch S. & L. R.W. | ||
| Kishacoquillas Valley R.R. | ||
| Huntingdon & Broad Top Mountain R.R. | ||
| Bedford Division | Bedford & Bridgeport R.R. | |
| Tyrone Division | Lewisburg & Tyrone R.R. | |
| Tyrone Branch | ||
| Bald Eagle Valley R.R. | ||
| Tyrone & Clearfield R.W. | ||
| Altoona Division | Altoona Yard | |
| Pittsburgh Division | ||
| Cambria & Clearfield Division | ||
| Cresson & Irvona R.R. | ||
| West Pennsylvania Division | Indiana Branch | |
| West Pennsylvania R.R. | ||
| Monongahela Division | P. V. & C. R.W. | |
| Philadelphia, Wilmington & Baltimore R.R. | Maryland Division | Washington Avenue |
| Baltimore & Potomac R.R. | ||
| Washington Southern R.W. | ||
| Central Division | ||
| Delaware Division | Delaware R.R. | |
| Baltimore & Delaware Bay R.R. | ||
| Northern Central Railway | Baltimore Division | |
| Susquehanna Division | ||
| Shamokin Division | Shamokin Valley & Pottsville R.R. | |
| Sunbury Division | Sunbury, Hazleton & Wilkes-Barre R.W. | |
| Elmira Division | E. & W. R.R. | |
| Erie Railroad | ||
| Canandaigua Division | E. & L. O. R.R. | |
| E. & L. O. R.R. Sodus Bay Branch | ||
| Philadelphia & Erie R.R. Division | Sunbury Division | North and West Branch R.W. |
| Eastern Division | ||
| Middle Division | ||
| Western Division | ||
