In January 2009, he lost in first round of the Qatar Open to Victor Hănescu and in the quarterfinals to del Potro. In second round of the Australian Open, he was crushed by Tommy Robredo, 6–1, 6–3, 6–0. After that, Troicki made a good result in the Zagreb Indoors. He lost in the semifinals to Marin Čilić, 2–6, 5–7. Also in February, Troicki won the GEMAX Open, a Tretorn Serie + Challenger held in Belgrade. In the final, he defeated Dominik Hrbatý in two sets.
In March 2009, Troicki played for the Serbian Davis Cup team, losing to David Ferrer 0–6, 3–6. He then competed in the next four Masters Series. In the BNP Paribas Open, he lost to David Nalbandian in the third round 4–6, 2–6. In the Miami Masters, he reached the fourth round before Andy Murray defeated him 6–1, 6–0. He then lost in the first round to Stan Wawrinka in the Monte Carlo Masters, and in the Rome Masters to Juan Martín del Potro in the second round. Viktor competed in the first tournament of his home nation in the Serbia Open, losing to compatriot Novak Djokovic. In the Madrid Masters, he lost to Nikolay Davydenko 2–6, 2–6, in the opener. He then represented Serbia in the ARAG World Team Cup, helping Serbia to win the title by beating Rainer Schüttler in the finals. In the French Open, he lost to fifth seed and eventual semifinalist Juan Martín del Potro in the second round 3–6, 5–7, 0–6, after defeating Łukasz Kubot in a tight five-setter 3–6, 6–3, 6–4, 6–7, 6–3, a match that lasted 3 hours and 58 minutes.
Troicki was seeded for the first time in a Grand Slam tournament in Wimbledon Championships, as 30th seed, beating Brian Dabul in straight sets in the first, and winning a five-setter against Daniel Gimeno-Traver in the second round. He lost to Andy Murray in the third round. He then competed in the German Open in Hamburg, losing to eventual finalist Paul-Henri Mathieu 0–3 ret., in the quarterfinals due to a foot injury he suffered when he fell hard in the start of the match. He then lost to Máximo González in Umag in the first round 4–6, 6–3, 6–7. He lost to Marc Gicquel in the second round of the Legg Mason Tennis Classic, 0–3 ret., due to his recurring foot injury suffered in Hamburg after receiving a bye in the first round. He then lost to Ferrer in the first round of the Rogers Masters 3–6, 0–6, and retired in the first round of the Western & Southern Financial Group Masters against Radek Štěpánek, 7–6, 1–0 ret. He had recorded five straight loses. Troicki competed in the US Open as 30th seed and claimed his first victory since Hamburg, defeating Peter Luczak 6–3, 6–3, 1–6, 2–6, 6–1, in the first round, but lost to Julien Benneteau in the following round. He then competed in the 2009 Davis Cup Play-offs, where he won both his matches against Uzbekistan.
Troicki reached another final in the Thailand Open. After defeating Thomaz Bellucci, 6–3, 7–6 in the round of 16, he then defeated eighth-seeded American John Isner 7–6, 6–2, in the quarterfinals. In his semifinal match, he went on to upset the defending 2008 Bangkok champion, 2008 Australian Open finalist, and top seed Jo-Wilfried Tsonga, 1–6, 6–2, 6–3 to reach his second ATP World Tour final to face the second seeded Gilles Simon. He lost 5–7, 3–6. He then competed in the 2009 China Open, where he lost in the second round to compatriot and eventual champion Novak Djokovic 3–6, 0–6. He then competed in the Shanghai ATP Masters 1000, where he lost to eighth seed Gilles Simon, 3–6, 4–6, after defeating Juan Mónaco 6–1, 6–2, in the first round. He was then upset by Karol Beck in the first round of the St. Petersburg Open, marking his 10th first-round loss in 25 tournaments. He then defeated Benjamin Becker 6–2, 7–6, before losing to Marin Čilić in the second round in a close three setter 6–7, 7–6, 6–7, in the Swiss Indoors. He played his last tournament in the BNP Paribas Masters, losing in the second round to Radek Štěpánek 4–6, 2–6, after defeating Paul-Henri Mathieu 7–6, 3–0 ret.