Murray played four tournaments during the North American summer hard court season. He was the runner-up at the Legg Mason Tennis Classic in Washington, D.C., where he was defeated by Arnaud Clement. He was a semifinalist at the ATP Masters Series event in Toronto and a quarterfinalist at the ATP Masters Series event in Cincinnati. At the latter tournament, Murray defeated Tim Henman in the first round and, in the second round, became one of only two players to defeat Roger Federer in 2006. Murray eventually lost to Roddick in the quarterfinals. Murray was ranked World No. 19 entering the final Grand Slam tournament of the year, the US Open. He won against World No. 11 Fernando Gonzalez in the third round before losing to World No. 6 Nikolay Davydenko in the fourth round 6–1, 5–7, 6–3, 6–0.

This was followed by his final Davis Cup appearance of the year, in which he won both singles rubbers in straight sets and lost the doubles en route to a British victory over Ukraine, which ensured the team's continued presence in group 1 of the Europe/Africa zone for 2007.

In his last four tournaments of the year, he lost to Henman in the first round of the Thailand Open. He reached the final of the doubles there, partnered by his brother. The following week at the tournament in Tokyo, Murray lost in the second round after receiving a first round bye. Murray defeated World No. 3 Ivan Ljubičić in the second round of the ATP Masters Series tournament in Madrid before losing to Novak Djokovic in the third round. Murray also lost in the third round of his last tournament of the year, the ATP Masters Series tournament in Paris.

Murray ended the year at World No. 17, his career best to that point