On July 4, 2008, Hendrick Motorsports owner Rick Hendrick and Martin announced that he would replace Casey Mears in the No.
5 car for the 2009 season, running a full-time schedule for the first time since 2006.
Martin signed a two-year contract with Hendrick, with a full-time schedule for 2009 and 2010.
Martin grabbed his first pole since 2001 at the Kobalt Tools 500 at Atlanta, and followed up with back-to-back poles in the following week at Bristol.

On April 18, 2009, Martin became the fourth driver to win a Cup race in NASCAR after turning 50, winning the 2009 Subway Fresh Fit 500 at Phoenix from the pole position.
The other three were Bobby Allison, Morgan Shepherd (twice), and Harry Gant (8 times, last in 1992).
His win snapped a 97-race winless streak going back to 2005.
After the victory, he did a Polish Victory Lap as a tribute to his late friend Alan Kulwicki, at the place where Kulwicki did his first Polish Victory Lap.
At Darlington, it was announced after the Richmond race that Martin would drive full-time again in 2010; Martin would go on to win the Southern 500.
 It was his first multiple-win season since 1999.
In the 2009 LifeLock 400, Martin won his third race of the season when Jimmie Johnson and Greg Biffle ran out of fuel in the last two laps while Martin had strategically conserved fuel and stayed back in third waiting for the leaders to run out.
 Martin added a series-leading fourth win at the LifeLock.com 400 at Chicagoland in July, holding off a charging Jeff Gordon.
 Because he and teammate Gordon also finished 1–2 at the LifeLock 400 at Michigan in June, LifeLock will pay a $1 million bonus to a family in Colorado.
Despite his series-leading four wins, due to some early season troubles, including two engine failures, a blown tire, and getting caught up in multi-car wrecks at Talladega and Daytona, Martin had struggled to get into the top 12, moving up two spots to 11th place with the win at Chicagoland Speedway.
 Martin also got his fifth pole of the 2009 season at Bristol Motor Speedway for the Sharpie 500.

After being on the Chase bubble for most of the season, Martin qualified for the 2009 Chase, as he was in sixth place in the standings following the Chevy Rock & Roll 400.
Because he led the Chase drivers in wins, with four, the Chase reseeding process moved him up five places and made him the points leader.

On September 20, he won his 40th and final career victory in Cup competition by taking the Sylvania 300 at New Hampshire in the first race of the Chase.
The win broke Martin's tie with Kyle Busch for the series wins lead and marked the third and final time in his career that he had won at least five times in a season (1993 and 1998).
Martin extended his lead to 35 points over Jimmie Johnson and Denny Hamlin, who were tied for second in the standings.

At the end of the 2009 AMP Energy 500 at Talladega, Martin was involved in a frightening crash in the last laps when he turned after contact with Martin Truex, Jr. and Juan Pablo Montoya, and flipped over one and a half times.
It was the second time Martin had ever been upside down in his racing career.
Once righted, Martin managed to drive his car back to pit road.
The wreck essentially ended his championship hopes according to experts.

Entering the season finale at Homestead-Miami Speedway, Martin and Johnson were the only drivers still able to win the 2009 Sprint Cup championship.
Martin finished 12th in the race, which was not enough to overcome Johnson's lead.
Martin again finished second in the standings, for the fifth and final time in his career.
On July 4, 2008, Hendrick Motorsports owner Rick Hendrick and Martin announced that he would replace Casey Mears in the No. 5 car for the 2009 season, running a full-time schedule for the first time since 2006. Martin signed a two-year contract with Hendrick, with a full-time schedule for 2009 and 2010. Martin grabbed his first pole since 2001 at the Kobalt Tools 500 at Atlanta, and followed up with back-to-back poles in the following week at Bristol.
On April 18, 2009, Martin became the fourth driver to win a Cup race in NASCAR after turning 50, winning the 2009 Subway Fresh Fit 500 at Phoenix from the pole position. The other three were Bobby Allison, Morgan Shepherd (twice), and Harry Gant (8 times, last in 1992). His win snapped a 97-race winless streak going back to 2005. After the victory, he did a Polish Victory Lap as a tribute to his late friend Alan Kulwicki, at the place where Kulwicki did his first Polish Victory Lap. At Darlington, it was announced after the Richmond race that Martin would drive full-time again in 2010; Martin would go on to win the Southern 500.  It was his first multiple-win season since 1999. In the 2009 LifeLock 400, Martin won his third race of the season when Jimmie Johnson and Greg Biffle ran out of fuel in the last two laps while Martin had strategically conserved fuel and stayed back in third waiting for the leaders to run out.  Martin added a series-leading fourth win at the LifeLock.com 400 at Chicagoland in July, holding off a charging Jeff Gordon.  Because he and teammate Gordon also finished 1–2 at the LifeLock 400 at Michigan in June, LifeLock will pay a $1 million bonus to a family in Colorado. Despite his series-leading four wins, due to some early season troubles, including two engine failures, a blown tire, and getting caught up in multi-car wrecks at Talladega and Daytona, Martin had struggled to get into the top 12, moving up two spots to 11th place with the win at Chicagoland Speedway.  Martin also got his fifth pole of the 2009 season at Bristol Motor Speedway for the Sharpie 500.
After being on the Chase bubble for most of the season, Martin qualified for the 2009 Chase, as he was in sixth place in the standings following the Chevy Rock & Roll 400. Because he led the Chase drivers in wins, with four, the Chase reseeding process moved him up five places and made him the points leader.
On September 20, he won his 40th and final career victory in Cup competition by taking the Sylvania 300 at New Hampshire in the first race of the Chase. The win broke Martin's tie with Kyle Busch for the series wins lead and marked the third and final time in his career that he had won at least five times in a season (1993 and 1998). Martin extended his lead to 35 points over Jimmie Johnson and Denny Hamlin, who were tied for second in the standings.
At the end of the 2009 AMP Energy 500 at Talladega, Martin was involved in a frightening crash in the last laps when he turned after contact with Martin Truex, Jr. and Juan Pablo Montoya, and flipped over one and a half times. It was the second time Martin had ever been upside down in his racing career. Once righted, Martin managed to drive his car back to pit road. The wreck essentially ended his championship hopes according to experts.
Entering the season finale at Homestead-Miami Speedway, Martin and Johnson were the only drivers still able to win the 2009 Sprint Cup championship. Martin finished 12th in the race, which was not enough to overcome Johnson's lead. Martin again finished second in the standings, for the fifth and final time in his career.
Mark Martin