- Jun 1 1st skirmish in US Civil War at Fairfax Court House, Virginia
- Jun 1 British territorial waters & ports off-limits during Civil War
- Jun 1 Skirmish at Arlington Mills, Virginia
- Jun 1 US & Confederacy simultaneously stop mail interchange
- Jun 3 1st American Civil War land battle: Union forces defeat the Confederacy at Philippi in modern-day West Virginia
- Jun 5 Federal marshals seize arms and gunpower at Du Pont works DE
- Jun 6 Lincoln's cabinet declares Union government will pay for expenses once states have mobilized volunteers
- Jun 8 American Civil War: Tennessee votes to secede from the Union
- Jun 8 US Sanitary Commission is given executive approval
- Jun 10 Battle of Big Bethel Virginia (Bethel Church, Great Bethal) the Union retreats
- Jun 11 Battle of Laurel Hill, West Virginia - Confederate General Robert S. Garnett is the first general killed during the Civil War
- Jun 12 Missouri Governor Claiborne Jackson calls for 50,000 volunteers to stop Federal "invasion" from taking over his state after US Army forces led by Nathaniel Lyon arrest pro-Confederate state militia at Fort Jackson
Harpers Ferry Evacuated
Jun 14 Confederates burn the B&O Railroad bridge and the US Armory buildings at Harpers Ferry before evacuating in face of General George McClellan's advance [1]
- Jun 15 Johnston evacuates Harpers Ferry
- Jun 16 Battle of Vienna, Virginia and Secessionville, South Carolina (James Island)
- Jun 17 Battle of Boonville, MI-Brigadier General Lyon defeats Confederate forces
- Jun 19 Anaheim Post Office established
- Jun 19 Francis Pierpont is elected provisional governor of West Virginia
- Jun 24 Battle of Mathias Point, Virginia Union forces attack Confederate batteries
- Jun 24 Tennessee becomes 11th (& last) state to secede from Union
- Jun 28 Leipzig Observatory discovers short-period (6.2 yrs) Comet d'Arrest
- Jun 30 CSS Sumter slips past USS Brooklyn blockade