The Cambodian leader said he was rewarding Southeast Asian Games athlete Bou Samnang "to encourage perseverance."
A soaked Bou Samnang broke down in tears after crossing the finish line in the 5,000m all alone on Monday nearly six minutes after the race winner.
Her resolve made her the toast of Games host Cambodia and footage of her wet, lonely run to the line was shown at home and overseas.
Hun Sen, currently attending a regional summit in Indonesia, added to the outpouring of admiration.
"The interesting story is that runner Bou Samnang ran in the rain until the finishing line although she did not place (in the medals)," he wrote in a statement.
"To encourage perseverance, I and my wife donate $10,000 to her."
The average worker earns about $10 a day in Cambodia.
The SEA Games in the capital Phnom Penh end on May 17.