The film centers around the romance between the Muslim Mughal Emperor Akbar, played by Hrithik Roshan and his Hindu wife, Jodhabai, played by Aishwarya Rai, although in reality Akbar's wife was never known as Jodhabai. The music is composed by acclaimed music composer A. R. Rahman.

Jodhaa Akbar is a sixteenth century love story about a marriage of alliance that gave birth to true love between a great Mughal emperor, Akbar, and a Rajput princess, Jodhaa.

Political success knew no bounds for Emperor Akbar (Hrithik). After having secured the Hindu Kush, he furthered his realm by conquest until his empire extended from Afghanistan to the Bay of Bengal, and from the Himalayas to the Godavari River. Through a shrewd blend of diplomacy, intimidation and brute force , Akbar won the allegiance of the Rajputs. But little did Akbar know that when he married Jodhaa (Aishwarya), a fiery Rajput princess, in order to further strengthen his relations with the Rajputs, he would in turn be embarking upon a new journey – the journey of true love.