Hrithik Roshan had a very "filmy" horse. The horse used to know what words like action meant and so when she heard action, she would take off, even if the scene required her to be stationary. Hence the crew would use other words instead of action to avoid the horse taking off. The names of his horses were Chandni and Superman.
In order to acquaint himself with the elephant and strike a comfort level, Hrithik Roshan used to travel to Karjat on days when he was not shooting, just to spend time with the elephant and feed her bananas at lunch. He called him Sweety pie and she would recognize his voice and his cologne.
Art director Nitin Desai created little cottages for Hrithik Roshan and Aishwarya Rai at his studio because Director Ashutosh Gowariker wanted the actors to stay in Karjat, where they were filming, rather than have them commute from Mumbai every day. They had all the comforts of home in the cottage. Hrithik's wife and son also stayed with him at the cottage.
During the first schedule in Rajasthan, the dressing of extras would begin at 5am and take almost 5 hours to complete the task. All these extras were Rajasthani's who knew no English at all, yet during the course of the shooting, they started learning words like first pass, second pass, action. Etc. They were extremely well behaved and soon became like junior actors.
The district administration imposed a ban on the screening of Jodhaa Akbar in Ambala, India following protests by members of the Rajput community who alleged that historical facts had been distorted in the film. They believe that Jodhaa was Akbar's daughter-in-law and not his wife.
Ila Arun plays the character of Maham Anga which is a stark contrast to her personality. So after portraying the very stern character for the film, she would feel terribly shy and immediately return to her trailer.
Director Ashutosh Gowariker on casting his 2 title characters: "When I heard the story the first time straightaway the two names, the two faces, that came to my mind were Hrithik and Aishwarya. I've been an admirer of their work right from their very first films, be it Kaho Naa... Pyaar Hai (2000) or ...Aur Pyaar Ho Gaya (1997). I have been fascinated by the way they have actually sculpted their graphs -- especially with a character like Rohit, which he did in Koi... Mil Gaya (2003). I thought that he is experimenting a lot, while staying within mainstream, with the type of characters he wants to portray. And for Aishwarya it was a Chokher Bali (2003) or a Raincoat (2004). I could see that even she was attempting to take up different kind of stuff."
While shooting in Sambhar (Faloti village) in June, sandstorms would occur at intervals of half hour. The unit could see the sandstorm coming 2-3 minutes away and they would only stop when it was half a minute away, then immediately take cover and then come back to shoot as soon as the storm would pass. This would happen every half hour. Hritik Roshan was a part of that sequence - the Ajmer Sharif scene.