Baker was born June 8, 1900, to a poor black family of sharecroppers and raised near Cuthbert, Georgia. Her family moved to the county seat when she was a child. As a youth, she worked for a farmer named J.A. Cox, chopping cotton.  By the 1940s, Baker was the mother of three children and worked as a maid to support her family.  In 1944, Baker started working for Ernest Knight, who had broken his leg. He owned a gristmill and held her there for days at a time against her will. One night they had an argument in which he threatened her with an iron bar. She tried to escape and shot and killed him. She immediately reported the incident and said she had struggled in self-defense.  Lena Baker was charged with capital murder and stood trial on August 14, 1944. The trial was presided over by Judge William “Two Gun” Worrill, who kept a pair of pistols on his judicial bench in plain view. The all-white, all-male jury convicted her by the end of the afternoon. Because blacks had been disenfranchised since the turn of the century in the South and could not vote, they were disqualified from jury service. After filing an appeal in the case, her court-appointed counsel, W.L. Ferguson, dropped Baker as a client.  Governor Ellis Arnall granted Baker a 60-day reprieve so that the Board of Pardons and Parole could review the case, but it denied clemency in January 1945. Baker was transferred to Reidsville State Prison on February 23, 1945.

Initially she was buried in an unmarked grave behind Mount Vernon Baptist Church. Members of the congregation in 1998 arranged to have a simple head stone placed at her grave.  In 2001, members of Baker’s family began to mark the anniversary of her death at her gravesite. Baker’s grand-nephew, Roosevelt Curry, requested the pardon in 2003, aided by the Georgia-based prison advocacy group, Prison and Jail Project. This was granted in 2005, with the Parole Board granting Baker a full and unconditional pardon. Commentators suggested that the Board of Pardons and Parole should have revised the charge as manslaughter in 1945, which would have carried a maximum 15-year sentence.