Lindh was sentenced to 20 years in prison after pleading guilty in 2002 to serving in the Taliban army, which violated U.S. economic sanctions against Afghanistan at that time.
At a news conference in San Francisco, Lindh's mother Marilyn Walker asked the president to show mercy during the Christmas season by commuting her son's sentence.
"John made a mistake in joining the Taliban," she said.
Lindh, who was born and raised in San Francisco suburb of Marin County, converted to Islam when he was 16 and traveled to Yemen, Pakistan and Afghanistan in furtherance of his religious studies, his lawyer Jim Brosnahan said at the news conference.
Lindh was captured by Northern Alliance forces in Afghanistan on Dec. 1, 2001, and was shot and wounded during a prison uprising. He was later turned over to U.S. authorities. He is currently serving his sentence in a minimum-security prison in Terre Haute, Ind.
Lindh, 28, initially asked for a commutation in 2004 and his lawyers have filed new petitions each year since.
The U.S. Department of Justice has never acted on the previous petitions. A spokeswoman said Wednesday the latest request is under review.
Lindh and more than 2,000 other people, including junk bond king Michael Milken, media mogul Conrad Black and former Congressman Randy "Duke" Cunningham, have applied to the Justice Department seeking official forgiveness in the form of pardons or sentence commutations.