Weeks was born to Harrison Samuel Weeks, Sr. (April 5, 1845 – January 23, 1892) and Julia W. Weeks (née Shoemaker) (March 13, 1852 – November 28, 1930) whom married on January 14, 1874 in Fort Union, New Mexico.
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His parents met while his father was stationed at Fort Union, New Mexico as his mother's family was from nearby rural Mora County, New Mexico.
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Recognized as an expert on developing and producing artillery and other weapons, Flagler continued his Ordnance service after the war, including assignments at the Watervliet, Augusta, Rock Island, Fort Monroe, Fort Union, San Antonio, Frankford, and Watertown arsenals.
He served at Camp Date Creek, Fort McDowell, Camp Renon, Fort Whipple, Camp Halleck, and Fort Union, all in the extreme southwest, until June 1870, during which time he saw considerable field service against Native Americans.