This is one of the most important temples in Vrindavana. The original Deity was hand carved by Rupa Goswami and given as a gift to his beloved disciple, Jiva Goswami, who later built a temple here. The Deity was first worshipped in the year 1542. The land was later acquired in 1558 when the Deity was installed on the simhasana (throne). The original Deity was moved to Jaipur when Aurangzeb attacked Vrindavana in 1670. The Deity now being worshipped is the pratibhu-murti (replica) and is considered nondifferent from the original Deity.
Formerly this spot was in the middle of Seva-kunja and it was the bhajana place of Rupa Goswami. He would daily hold discourses on the Srimad Bhagavatam and Krishna's pastimes here with the other Goswamis and their close associates. Srila Prabhupada said that Radha-Damodara temple is in the centre of the spiritual world, because of the transcendental activities that went on here amongst the followers of Lord Chaitanya, led by Srila Rupa Goswami.

Besides the Deities of Sri Sri Radha Damodara, also kept in this temple are the Deities originally worshipped by Krishnadasa Kaviraja (Radha Vrindavana-candra), Jayadeva Goswami (Radha Madhava), Bhurgarbha Goswami  (Radha Chalachikan), as well as the govardhana-sila of Srila Sanatana Goswami which has the footprint of Lord Krishna impressed upon it.

It so happened that Sanatana Goswami used to circumambulate Govardhana hill everyday as part of his daily vows; even in his old age. One day, Lord Krishna in the guise of a beautiful cowherd boy, suddenly appeared before Sanatana Goswami, and requested him that now you are very old, there is no need to go round Govardhana hill everyday.

Sanatana replied that as he had taken such a vow to daily circumambulate Govardhana, he could not stop. Understanding Sanatana's determination, Krishna then stood on a big stone from the hill and started playing His flute. The flute playing of the Lord was so enchanting, that the stone started to melt and Krishna's footprint got impressed upon it and also the hoof print of a calf, along with Krishna's flute and His stick used for herding cows. Krishna then gave this stone from Govardhana hill to Sanatana and told that if he circumambulated this govardhana-sila four times, it would be equal to going round Govardhana Hill. Sanatana then accepted the sila from Krishna, and from that time on, he circumambulated this sila, instead of going all the way around Govardhana hill. One can have darsana of this sacred govardhana-sila by asking the pujari and giving a small donation.

Behind the Radha Damodara Temple is the Samadhi of Sril Rupa Goswami

Srila Rupa Goswami entered samadhi in the year 1564 and his sacred body was entombed at this very site by his beloved disciple and nephew Jiva Goswami. Rupa Goswami first arrived in Vrindavana along with his elder brother Sanatana Goswami in the year 1516, after receiving the direct order of Lord Chaitanya to proceed to Vrindavana and fulfill four specific tasks. Firstly, to excavate the lost holy sites of Lord Krishna's pastimes in and around Vrindavana. To construct temples dedicated to Radha and Krishna, and also establish the rules and regulations of deity worship. And lastly, to compile books on the transcendental process of Bhakti-yoga, the science of devotional service to the Lord. Through his writings Srila Rupa Goswami chalked out the perfect spiritual path for all the followers of Lord Chaitanya down through the ages.

Rupa Goswami first met Lord Chaitanya at Ramakeli in 1514, and along with his brothers Sanatana and Anupama, completely surrendered to the lotus feet of the Lord. At that time all three brothers were employed as important ministers in the Mohammedan government of Bengal under Hussain Shah. Lord Chaitanya assured them that now they had surrendered to Krishna, they would soon be delivered and would be able to join the sankirtana movement. After some months both Rupa and Anupama were freed from service, unfortunately Sanatana was not so lucky and was thrown in jail, but by the grace of Lord Krishna, he also got free from the clutches of Hussain Shah.

It was Rupa Goswami who more than anyone else, firmly established the sankirtana movement of Lord Chaitanya. He wrote a large number of important books on the science of bhakti-yoga and after the disappearance of Lord Chaitanya in 1534, Rupa became the undisputed leader of all the Gaudiya Vaisnavas in the world. Even today all Gaudiya Vaisnavas are known as Rupanugas, or followers of Srila Rupa Goswami most famous book is Bhakti-rasamrta-sindhu (The Ocean of the Nectar of Devotion) which must be read by all aspiring Vaisnvas and forms the solid foundation of the bhakti movement of Lord Chaitanya. The essence of this book was explained directly to Rupa by Lord Chaitanya during their historic meeting at Prayag (Allahabad) in 1516. After teaching Rupa all the important aspects of devotional service, the Lord sent him to Vrindavana to compile books on these very teachings.

After spending some time in Vrindavana, Rupa and Anupama left to visit Lord Chaitanya in Puri, it is believed that on this long and arduous journey Anupama left his body. On his way to Puri, Rupa Goswami started to write a drama about Lord Krishna's pastimes in Vrindavana and Dwaraka. On arrival at a village named Satyabhamapur in Orissa, he had a dream that a beautiful woman appeared before him and asked him to write a separate drama about her. When Rupa awoke the next morning he realized that she was Lord Krishna's most possessive queen, Satyabhama, and decided to write a separate drama about Dwaraka. On Rupa's arrival at Jagganatha Puri, he met Lord Chaitanya and showed the Lord the outline of his two dramas. The Lord confirmed that writing two dramas mixing the lilas of Vrindavana and Dwaraka was not proper as their was a vast difference between them. In Vrindavana the Lord enjoys the madhurya-rasa, where as in Dwaraka He enjoys the Swakiya-rasa. Lord Chaitanya as well as Ramananda Raya were delighted to read the early drafts of these two dramas, which were eventually called Vidagdha Madhava and Lalita Madhava respectively. These two works are considered by Gaudiya Vaisnavas to be the most important dramatic literatures in the Sanskrit language. Rupa Goswami stayed ten months in Puri and received further instructions on devotional service from Lord Chaitanya. The Lord then asked Rupa to proceed to Vrindavana and complete the task of rediscovering the lost holy places of Lord Krishna's pastimes. On returning to Vrindavana, Rupa Goswami discovered at Brahma Kunda the Deity of Vrndadevi, from who the town of Vrindavana takes its name, this Deity was later moved to Kamyavana. Rupa Goswami then discovered the famous Govindaji Deity and immediately established Lord Govindaji's worship on a grand scale. On hearing the good news of Rupa's progress, Lord Chaitanya sent some of his best men to assist Rupa in serving the Deity of Govindaji and establishing the Lord's mission in Vrindavana. Shortly Rupa and Sanatana Goswamis were joined by Ragunatha dasa Goswami, Gopal Bhatta Goswami, Raghunatha Bhatta Goswami and Srila Jiva Goswami. These great personalities become famous as the six Goswamis of Vrindavana. Jiva Goswami, who was the son of Rupa's brother Anupama, became the most important disciple of Rupa Goswami.

Srila Rupa Goswami was an incarnation of Rupa Manjari, the most important of the eight confidential maidservants of Srimati Radharani in the spiritual world. It is said that without taking shelter of Srila Rupa Goswami one cannot enter into the pastimes of Lord Chaitanya, and without taking shelter of Rupa Manjari one cannot enter into the confidential loving pastimes of Sri Sri Radha and Krishna.