Arjun: The Warrior Prince is based on the early life of the Prince Arjuna, loosely taken from the ancient Indian epic Mahabharata. The storyline begins with Arjun as a nine-year-old boy, and follows him until he grows into the warrior that the world knows him as. It explores his life with his brothers in Hastinapur, his training and education, and his ultimate discovery of the warrior within himself.

The film begins with Uttar, the young prince of Viratnagar (Kingdom of king Virata), asking a maid (Brihannala) to tell him a story. The maid narrates him the story of Arjun.

She tells him that Arjun was a student of Drona, and that he learned the art of warfare from him. He was more skilled than all the students of Drona. None of his own brothers, nor his cousins - the hundred Kauravas - could equal him in the art. Duryodhana and the other Kauravas despised the Pandavas, for they feared that they might usurp Duryodhana's throne. When the king Dhritrashtra grew older, the rivalry between his sons, the Kauravas and the Pandavas intensified. Twice, Duryodhana attempted to kill all the Pandavas, but failed. To avoid further conflict, Dhritrashtra proclaimed Duryodhana as the crown prince of Hastinapur, and asked Yudhishthira to be the king of a distant unkempt territory of the empire.

In the meantime, Arjun won a swayamvar, and married the daughter of the King of Panchala, Draupadi. Duryodhana, who loathed the Pandavas, hatched a conspiracy with his uncle Shakuni and won all that belonged to the Pandavas in a betting game called chaupar. After losing everything, Yudhishthira betted his own brothers and Draupadi, and even himself. Draupadi was insulted in front of everyone, but Arjuna could not say anything because Yudhishthira was the king, and the king's words are the last words. The Pandavas, according to the rules of the game, had to go into exile for twelve years and an agyatavasa for one year. While all the Pandavas go one way, Arjuna travels North to do tapasya. Before leaving, Draupadi makes him promise that he will take revenge for her insult. He then leaves, and does tapasya, during which he earns a bow from the Lord Shiva.

The story then shifts back to the present day Viratnagar. It is revealed that the Pandavas are spending their secret exile, or 'agyatavasa', there, and are noticed by some of the spies of Duryodhana. According to the outcome of the game, if any one of the Pandavas is found before the end of that one year, the Pandavas will have to again go for a twelve-year exile. The spy informs Duryodhana that the Pandavas are in Viratnagar. So he launches an attack on Viratnagar with the help of his bandit friends. The king of Viratnagar leaves to thrash the marauding bandits. However, that is the bait. From the other direction, Duryodhana's army comes, and it seems that the young prince of Viratnagar is the only one who is left to fight.

Uttar's maid drives the young prince's chariot to the field, but the prince, distraught by the number of enemies, flees. The maid stops him, and reveals her true identity: the maid (Brihannala) comes out as Arjun. Arjun retrieves his bow and makes prince Uttar drive his chariot. The warrior massacres the army and emerges victorious, and at last, Arjuna alone defeats all Kaurava warriors, including Bhisma and Drona.