Harper had to leave the game against Double-A Akron because of the injury.
It occurred in the eighth inning, according to reports. Harper, who plays for Harrisburg, hurt his hamstring while running from first to third on an Archie Gilbert double. Harper had to be helped off the field.
"I'm not going to worry a whole lot about Bryce Harper down there with a slight pulled hammy," Nationals manager Davey Johnson said. "It's the end of the season. He probably won't play the rest of the year. You are not taking a chance aggravating it where it becomes a more serious injury."