He returned to acting by playing the lead role in the critically acclaimed Marathi comedy drama Ventilator (2016), which was produced by Priyanka Chopra.

His first film of the new millennium was the epic musical sports drama Lagaan, produced by and starring Aamir Khan alongside debutante Gracy Singh.

The film revolved around the people of a small village in Victorian India who stake their future on a game of cricket against their ruthless British rulers.

The story of the film revolves around an NRI project manager at NASA, who returns to India to discover the challenges faced by a rural village, and dedicates himself to their development, addressing issues of education, healthcare, and infrastructure.

[14] Gowariker's next screenwriting and directorial venture was the epic historical romantic drama Jodhaa Akbar (2008) starring Hrithik Roshan and Aishwarya Rai in lead roles.

Set in the 16th century, the film depicted the life and romance between the Muslim Emperor Akbar of Mughal Empire and the Hindu Princess Jodhaa Bai of Amber, who married him on a political marriage.

It opened to widespread critical acclaim upon release, with high praise for its direction, soundtrack, cinematography, costume design, choreography and performances of the cast.

[18] His next venture was the historical action-adventure Khelein Hum Jee Jaan Sey (2010) starring Abhishek Bachchan and Deepika Padukone in lead roles.

[19] After a 6-year hiatus, Gowariker made his comeback with the period action-adventure Mohenjo Daro (2016) starring Roshan (in their second collaboration) alongside debutante Pooja Hegde in lead roles.

[22] His next venture was the epic war drama Panipat (2019) starring Arjun Kapoor, Sanjay Dutt and Kriti Sanon in lead roles.