Construction of the main line westward to Pittsburgh began at once and progressed rapidly. By making use of the Alleghany Portage Railroad from Hollidaysburg, the Pennsylvania Railroad eventually secured a continuous line from Harrisburg to Pittsburgh. But between Philadelphia and Harrisburg passengers were for a long time subjected to many inconveniences. Finally in 1857 the Pennsylvania Railroad bought the Philadelphia and Columbia from the State, rebuilt it, and extended it to Harrisburg. At the same time the Pennsylvania bought the main line of the Public Works, which included the Alleghany Portage Railroad. On July 18, 1858, the first through train passed over the entire line from Philadelphia via Mount Joy to Pittsburgh without transfer of passengers. At the same time the first smoking car ever attached to a passenger train was used, and sleeping cars also soon began to appear.

The railroad genius identified with the history of the Pennsylvania Railroad during the following decade is J. Edgar Thomson. A man of vision and of great shrewdness and ability, he was more like the modern railroad head of the Ripley or Underwood type than of the Vanderbilt, Garrett, or Drew type. His interest was never in the stock market nor in the speculative side of railroading but was concentrated entirely on the development and operation of the Pennsylvania Railroad system. His dreams were not of millions quickly made nor of railroad dominance simply for the power that it gave; his mind was concentrated on the growth and prosperity of a vast railroad system which would increase with the years, become lucrative in its operations, and not only radiate throughout the State of Pennsylvania but extend far beyond into the growing West.

Under the Thomson management, which lasted until 1874, the record of the Pennsylvania Railroad was one of progress in every sense of the word. While Daniel Drew was lining his pockets with loot from the Erie Railroad and Commodore Vanderbilt was piling up his colossal fortune through consolidation and manipulation, J. Edgar Thomson was steadily building up the greatest business organization on the continent. In 1860, the entire Pennsylvania Railroad system was represented merely by the main line from Philadelphia to Pittsburgh, with a few short branches. By 1869 the road had expanded within Pennsylvania alone to nearly one thousand miles and also controlled lines northward to the shores of Lake Erie, through the State of New York.

But the master accomplishment of the Thomson administration was the acquisition of the Pittsburgh, Fort Wayne and Chicago line in 1869. This new addition gave the Company its own connection with Chicago and made a continuous system from the banks of the Delaware at Philadelphia to the shores of Lake Michigan, thus rivaling the far-flung Vanderbilt line, a thousand miles long, which the industrious Commodore was now organizing. Shortly thereafter the Pennsylvania began to expand on the east also and obtained an entry into New York City by acquiring the United Railroad and Canal Company, which owned lines across the State of New Jersey, passing through Trenton.

In the latter years of the Thomson management it became more and more evident that it was important for the Pennsylvania Railroad to have further Western connections which would reach the growing cities of the Middle West. While the Fort Wayne route made a very direct connection with Chicago and included branches of value, yet the keen competition which was developing in the expansive years following the Civil War made actual control of the Middle Western territory a matter of sound business policy. The Vanderbilt lines were reaching out through Ohio, Indiana, and Illinois; the Baltimore and Ohio was steadily developing its Western connections, and now Jay Gould had come actively on the scene with large projects for the Erie. To offset these projects, early in 1870 a "holding company"—probably the first of its kind on record—known as the Pennsylvania Company was formed for the express purpose of controlling and managing, in the interest of the Pennsylvania Railroad, all lines leased or controlled or in the future to be acquired by the Pennsylvania Railroad interests west of Pittsburgh and Erie. This Company took over the lease of the Fort Wayne route and also acquired control by lease of the Erie and Pittsburgh, a road extending northward through Ohio to Lake Erie.

After this date the expansion of the system west of Pittsburgh went on rapidly. In 1871 the Cleveland and Pittsburgh Railroad, which had been opened as early as 1852, came under the Pennsylvania control. Soon after this, many smaller lines in Ohio were merged in the system. The most important acquisition during this period, however, was the result of the purchase of the great lines extending westward from Pittsburgh to St. Louis, with branches reaching southward to Cincinnati and northward to Chicago. This system—then known as the "Pan Handle" route and later as the Pittsburgh, Cincinnati, Chicago and St. Louis was a consolidation of several independent properties of importance which had been gradually extending themselves over this territory during the previous decade. This new system, which embraced over fourteen hundred miles of road, gave the Pennsylvania a second line to Chicago, a direct line to St. Louis, a second line to Cincinnati, and access to territory not previously tapped.

While the achievements of the Pennsylvania Railroad Company during these years of consolidation and expansion are not to be compared with those of more modern times, it is well to realize that even as early as the seventh decade of the last century this railroad was always in the forefront in matters of high standards and progressive practice. It was the pioneer in most of the improvements which were later adopted by other roads. The Pennsylvania was the first American railroad to lay steel rails and the first to lay Bessemer rails; it was the first to put the steel fire-box under the locomotive boiler; it was the first to use the air brake and the block signal system; it was the first to use in its shops the overhead crane.

In these earlier years also the Pennsylvania had established its enviable record for conservative and non-speculative management. No railroad wrecker or stock speculator had ever had anything to do with the financial control of the company, and this tradition has been passed on from decade to decade. The stockholders themselves, even in those days of loose methods and careless finance, had the dominating voice in the affairs of the company and were also factors in the approval or disapproval of any proposed policies. In the matter of its finances the Pennsylvania developed and established an equally clean record. The company began almost at the beginning to pay a satisfactory dividend on its shares and continued to do so right through the Civil War period. Since the through line from Philadelphia to Pittsburgh was opened, not a single year has passed without the payment of a dividend—a sixty-year record which can be duplicated by no other American railroad system.

The Pennsylvania still continued to forge ahead even during the exciting period from 1877 to about 1889, when the trunk lines were aggressively carrying on that policy of cutthroat competition between Chicago and the Atlantic seaboard which resulted in so severely weakening the credit and position of properties like the Baltimore and Ohio and the Erie. The Pennsylvania, too, indulged in rate cutting, but the management was equal to the situation and made up in other directions what it lost in lower rates. It gave superior service, developed a high efficiency of operation, and steadily maintained its properties at a high standard. During these years the president was George B. Roberts, who had succeeded Thomas A. Scott in 1880.

Roberts's management spanned the period from 1880 to 1897 and embraced a decade of comparative prosperity for the country as a whole and nearly a decade of panic and industrial and financial depression. During the earlier decade the business of the Pennsylvania was continually benefited by the industrial development and growth which marked the period. It was at this time that the Pittsburgh district took its permanent place as the great center of steel and iron manufacture. The discovery of petroleum in western Pennsylvania, creating an enormous new industry in itself, proved to be an event of far-reaching significance for the Pennsylvania Railroad. The extensive opening up of the soft coal sections of western Pennsylvania, Ohio, and Indiana, also meant much for this great system of railroads.