The project was nicknamed "The Great Bore" by its critics, including future Supreme Court Justice Oliver Wendell Holmes Jr., who said that he would like to "wall up a dozen lawyers at one end of the tunnel and put a good fee at the other."

The most important proponent of the northern route and the Hoosac Tunnel was Alvah Crocker, a self-made paper mill owner from Fitchburg, Massachusetts.

In 1848, Crocker secured from the legislature a charter for the Troy & Greenfield Railroad (T & G), with provisions for a tunnel through Hoosac Mountain.

It successfully lobbied to block state funding of the tunnel in 1861, which bankrupted Haupt and temporarily stopped the project.

The state sent engineer Charles Storrow to Europe to study modern tunneling techniques, including the use of nitroglycerin and compressed air.

In 1863 the state, with Alvah Crocker now superintendent of railroads, restarted the project and made Thomas Doane the chief engineer.

Canadian engineer Walter Shanly (sometimes spelled Shanley) and his brother Francis took over the project from the state and remained through the completion of the tunnel boring.

[4] The final chief engineer was Bernard N. Farren, who took over on November 19, 1874, and on Thanksgiving Day that year, the last 16 feet (4.9 m) of rock was removed beneath the town of North Adams.

Workers were digging the tunnel's 1,028-foot (313 m) vertical exhaust shaft when a candle in the hoist building ignited naphtha fumes that had leaked from a "Gasometer" lamp.

A worker named Mallory was lowered into the shaft by a rope the next day; he was overcome by fumes and reported no survivors, and no further rescue attempts were made.

Several months later, workers reached the shaft's bottom and found that several victims had survived long enough to fashion a raft before suffocating.

The Boston, Hoosac Tunnel and Western Railway was organized in 1877 to build from near the Massachusetts–Vermont border, where state ownership ended, parallel to the Troy and Boston Railroad to near Johnsonville, New York and then west via Schenectady to Rotterdam Junction on what became the New York, West Shore, and Buffalo Railway in 1883.

In late 1878, the T&B attempted to evict the BHT&W from the roadbed of the abandoned Albany Northern Railroad between Hart's Falls and Eagle Bridge.

In May, 1879, a frog war was feared at Hoosick Junction, where the BHT&W was to cross the T&B's Troy and Bennington Railroad.

In July, Cornelius Vanderbilt, who owned the New York Central and Hudson River Railroad, acquired a controlling interest in the T&B, threatening to build a branch to Saratoga Springs unless the BHT&W/D&H alliance was ended.

Three years later, traffic within the tunnel was so heavy, at 70,000 cars a month, that the power plant in Adams, with its 6000 kW generator, could not keep up.

The last regularly-scheduled Boston and Maine Railroad passenger train, the Minute Man, passed through the tunnel in 1958.

Clearances were increased in 1997 and 2007, the former by lowering the track, the latter by grinding 15 inches (38 cm) off the roof,[15] allowing trailer on flat car (TOFC) and tri-level automobile carriers to pass.

In March 2012, the Federal Railroad Administration granted $2 million to the Massachusetts Department of Transportation for preliminary engineering to increase clearance in the tunnel for double stack container trains.

The Hoosac Tunnel on the Pan Am Southern (the Northern Route), used by NS prior to this agreement, is too low for double-stack trains.

Berkshire & Eastern Railroad (B&E), a wholly owned subsidiary of Genesee & Wyoming (G&W), will replace Springfield Terminal as the operator of Pan Am Southern and the tunnel.

CSX made specific commitments in its filings and entered into settlement agreements with numerous parties that had initially raised concerns about the transaction.