While a DNF at the Sandown 500 was a disappointment, Whincup and Davison achieved a very credible 9th place finish at the Bathurst 1000 after qualifying 29th and the highest of the three Castrol Commodore's.

He had many solid results throughout the season, including a fourth at the one-off Chinese round at the Shanghai International Circuit, a third at the Sandown 500 and most notably, second at the Bathurst 1000 endurance events with teammate Jason Richards after leading late in the race.

In 2007, Whincup returned with the same team which was re-branded TeamVodafone and celebrated several victories included a second Bathurst 1000 title alongside teammate Craig Lowndes and new engineer Mark Dutton.

Whincup began a mentoring role as part of TeamVodafone's Junior Development Program, and as a co-ambassador for Formula Ford Australia alongside Will Davison.

He celebrated both his 50th V8 Supercar Championship start and his inaugural pole position at Triple Eight Race Engineering's test track, Queensland Raceway.

Whincup then had a disappointing weekend at Desert 400 at the Bahrain International Circuit, where poor qualifying pace for Triple Eight was compounded by a run of all three races marred by minor accidents, and he took away zero points.

Whincup won both races, and headed into the Grand Finale at Phillip Island on the 1–2 December weekend with a slender seven point championship lead.

After the final race Whincup finished second, behind Todd Kelly and two places ahead of Tander but fell just two points short of the title.

[8] In 2009, Whincup successfully defended his title in a brand new Ford FG Falcon, including wins at Adelaide, Hamilton, Tasmania, Darwin, Townsville, Oueensland, Phillip Island and Barbagallo.

Despite bad luck in the endurance races and at the Gold Coast, Whincup was able to put it all together at Sydney Olympic Park and became the first back-to-back championship winner since Marcos Ambrose in 2003–2004.

Whincup won the first four races of the season[10] and Hamilton but a run of bad luck at Queensland raceway and Winton saw him relinquish the championship lead for the first time in two years, and sat second in the points table, just ahead of teammate Craig Lowndes in third.

He went on to once again eclipse Lowndes in the points table, and earn himself a fifth title, putting himself alongside Ian Geoghegan, Dick Johnson and Mark Skaife in terms of championship successes.

After a final lap battles with Mark Winterbottom in 2013, this time he lost out to Ford Performance Racing teammate Chaz Mostert as he ran low on fuel.

[14] During 2015 at Bathurst, Whincup had led the race mid-way through, only to wind up behind team-mate Lowndes thanks to a throttle sensor problem that required a long stop.

Whincup misread a call which ultimately saw him illegally pass the Safety Car going up Mountain Straight as the critical final pitstops were unfolding.

At the Bathurst 1000, Whincup would fail to win despite being the first to cross the finish line, due to a time penalty following a collision with Scott McLaughlin and Garth Tander.

Whincup and Triple Eight were in the shadow of Dick Johnson Racing Team Penske being out qualified and outraced by their drivers Scott McLaughlin and Fabian Coulthard.

On 16 September, Whincup and a co-driver Dumbrell led from start to finish and sweep of the Sandown 500 podium for a dominant Triple Eight Holden squad, as Enduro Cup kicked off.

On Race 24 at Pukekohe, Whincup was incorrectly picked up by the Safety Car despite being further back in the field due to having already taken his first compulsory pit stop, which prompted him to pass it without permission.

[26][27] At the final round of the Bathurst 1000, Whincup battling with Brodie Kostecki and Chaz Mostert when he ran wide at The Cutting and hit the wall on Lap 33.

[28] On 5 February 2017, Whincup drove in and won his first ever GT race when he teamed with Lowndes and Finnish driver Toni Vilander to win the 2017 Liqui Moly Bathurst 12 Hour driving a Ferrari 488 GT3 for Maranello Motorsport.