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Judah went to work on a number of railroads in the Northeast, including engineering for the Niagara Gorge Railroad. He was elected member of the American Society of Civil Engineers on May 1853.

Judah was hired in 1854 at age 28 as the Chief Engineer for the Sacramento Valley Railroad in California. He and his wife Anne sailed to Nicaragua, crossed over to the Pacific, and caught a steamer to San Francisco. Under his charge, it became the first common carrier railroad built west of the Mississippi River.

On January 1857 in Washington DC, Judah published "A Practical Plan for Building The Pacific Railroad", in which he outlined the general plan and argued for the need to do a detailed survey of a specific selected route for the railroad, not a general reconnaissance of several possible routes that had been done earlier.

Nominated in the 1859 California Pacific Railroad Convention in San Francisco, Judah was sent to Washington DC to lobby in general for the Pacific Railroad. Congress was distracted by the trouble of pre-Civil War America and showed little interest. He returned noting that he had to find a specific practical route and some private financial backing to do a detailed engineering survey.

In 1860, he set out to make general reconnaissance studies, using a barometer to measure elevation, of several possible routes through the Sierra. That Fall, with the help of Daniel W. Strong, a storekeeper in Dutch Flat, California, Judah found a practical trans-Sierra railroad route. In November 1860, Judah published "Central Pacific Railroad to California", in which he declared "the discovery of a practicable route from the city of Sacramento upon the divide between Bear River and the North Fork of the American, via Illinoistown (near Colfax), Dutch Flat, and Summit Valley (Donner Pass) to the Truckee River". He advocated the chosen Dutch Flat-Donner Pass route as the most practical one with maximum grades of one hundred feet per mile and 150 miles shorter than the route recommended in the government's reports. Much of the Sierra Nevada where the practical routes were located was double-ridged, meaning two summits separated by a valley, Donner Pass was not and thus was more suitable for a railroad. From Dutch Flat, the Pacific road would climb steadily up the ridge between the North Fork American and Bear Rivers to the Pass before winding down steadily following the Truckee River out of the mountains into the Great Basin of Nevada.

Judah's youthful interest in the general subject of a Pacific Railroad developed during this period into almost an obsession, his wife observing that...

Everything he did from the time he went to California to the day of his death was for the great continental Pacific railway. Time, money, brains, strength, body, and soul were absorbed. It was the burden of his thought day and night, largely of his conversation, till it used to be said 'Judah's Pacific Railroad crazy,' and I would say, 'Theodore, those people don't care,' or 'you give your thunder away.' He'd laugh and say, 'But we must keep the ball rolling.  Wheat, A Sketch of the Life of Theodore D. Judah (1925)

Failing to raise funds for the Central Pacific project in San Francisco, Judah succeeded in signing up five Sacramento merchants, : James Bailey, Leland Stanford, Collis P. Huntington, Mark Hopkins, and Charles Crocker. On June 28, 1861, the Central Pacific Rail Way of California (CPRR) was incorporated with Judah as the chief engineer. Judah had the CPRR backing to survey the route over the Sierra Nevada along which the railroad was to be built during the 1860s, as well as barometric reconnaissance of two other routes, which turned out to be inferior. In a report dated October 1, 1861, Judah discussed the results of the survey, the merits of the chosen Dutch Flat-Donner Pass route, and the estimated costs from Sacramento to points as far as Salt Lake City.

On October 9, 1861, the CPRR directors authorized Judah to go back to Washington DC, this time as the agent of CPRR, to procure "appropriations of land and U.S. Bonds from the Government to aid in the construction of this road". The next day, Judah published a strip map (a.k.a. the Theodore Judah map), 30 inches tall by 66 feet long, of the proposed alignment of the Central Pacific Railroad.   On October 11, 1861, Judah boarded a steamer in San Francisco headed for Panama.

At Washington DC, Judah began an active campaign for a Pacific Railroad bill. He was made the clerk of the House subcommittee on the bill and also obtained an appointment as secretary of the Senate subcommittee. On July 1, 1862, President Lincoln signed the Pacific Railroad Act into law, which authorized the issuance of land grants and U.S. bonds to CPRR and the newly chartered Union Pacific Railroad for the construction of a transcontinental railroad. Judah then went to New York to order supplies and sailed back to California on July 21, 1862, having accomplished his mission in less than a year. 

Judah died of yellow fever on November 2, 1863. He contracted the disease in Panama on a voyage with his wife to New York City, apparently becoming infected during their land passage across the Isthmus of Panama. He was traveling to New York to seek alternative financing to buy out the major investors. He died before his dream of a transcontinental railroad could be completed.