The message, from Alfred Vail to Samuel F. B. Morse, announced that the Whig Party candidate would be Henry Clay, and his running mate would be Theodore Frelinghuysen.

Traveling in secret to avoid an assassination plot in Baltimore, Abraham Lincoln passed through Annapolis Junction en route to Washington for his 1861 inauguration.

[13] In 1863, Annapolis Junction formed the northern boundary of coverage for the XXII Corps (Union Army) Department of Washington, and became the rendezvous point for drafted men from Maryland.

[15] In a letter to the editor, on July 24, 1864, the writer complains that the 65 troops did not run off, but instead were following orders of Mag Gen. Ord to leave the area before the arrival of the entire rebel army.

[17] In 1867, the First Regiment of the Lincoln Zouaves Corps de Afrique held a political rally at Annapolis Junction with 400 musketmen listening to radical speeches from J.J Stewart, Judge Bond, and others.

The train was a night express carrying President Ulysses S. Grant, his wife, and the Secretary of Treasury George S. Boutwell, who all escaped uninjured.

[22] In June, 1917, Secretary of War Newton D. Baker announced that 17,000 acres (69 km2) would be bought at Annapolis Junction to accommodate a National Army Cantonment to train 40,000 to 60,000 men for at least one year.

On October 7, 1919, the post office for Annapolis Junction moved back to the Anne Arundel side of the tracks, only to return to Howard County in September 1921.

Few residents call Annapolis Junction "home," more frequently associating themselves with adjacent Savage, its southern neighbor Laurel, or Fort Meade.

In 2014, Howard County executive Ken Ulman announced that the park and ride land would be sold to private developers in order to increase the tax base.

[30] Colfax Corporation a major welding, air and gas handling equipment, and medical devices manufacturer is based in Annapolis Junction.