Jodhaa Akbar is a sixteenth-century love story about a political marriage of convenience between a Mughal emperor, Akbar, and a Rajput princess, Jodhaa.

Political success knew no bounds for Emperor Akbar (Hrithik Roshan). After having secured the Hindu Kush, his empire extends from Afghanistan to the Bay of Bengal, to the Narmada River. Through a shrewd blend of diplomacy, intimidation and brute force, Akbar won the allegiance of the Rajputs. This allegiance was not universal. But little did Akbar know that when he married Jodhaa (Aishwarya Rai), 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.

The daughter of King Bharmal of Amer, Jodhaa resented being reduced to a mere political pawn in this marriage of alliance, and Akbar's biggest challenge now lies in winning the love of Jodhaa – a love hidden deep below resentment and extreme prejudice.

Many of the events portrayed in the movie are based on real events. Certain Rajput groups claimed Jodhaa was married to Akbar's son, Jahangir, not Akbar. The film was not released in 30 cinema theatres in Rajasthan.

Several historians claim that Akbar's Rajput wife was never known as "Jodha Bai" during the Mughal period. According to Professor Shirin Moosvi, a historian of Aligarh Muslim University, neither the Akbarnama (a biography of Akbar commissioned by Akbar himself), nor any historical text from the period refer to her as Jodha Bai. Moosvi notes that the name "Jodha Bai" was first used to refer to Akbar's wife in the 18th and 19th centuries in historical writings. In Tuzk-e-Jahangiri, she is referred as Mariam Zamani.

According to historian Imtiaz Ahmad, the director of the Khuda Baksh Oriental Public Library in Patna, the name "Jodha" was used for Akbar's wife for the first time by Lieutenant-Colonel James Tod, in his book Annals and Antiquities of Rajasthan. According to Ahmad, Tod was not a professional historian.N. R. Farooqi claims that Jodha Bai was not the name of Akbar's Rajput queen; it was the name of Jahangir's Rajput wife.

Ashutosh Gowarikar's reaction was,

While making the film I did my best to go by the book. I consulted the best historians and went through the most rigorous research. And there are different names used for Akbar's wife, Jodhaa being one of them. In fact, there's a disclaimer about the Rajput queen's name at the beginning of the film. But to see that, the protesters have to see the film.