The history of the Kathmandu Valley, according to legend, begins with Swayambhu, or the "the self-existent." In times uncharted by history, Bodhisattva Manjusri came across a beautiful lake while traveling. He saw a lotus, with thousand golden petals, diamonds pistils, ruby anthers, and lapis lazuli stalk. It emitted brilliant light at the lake's center, so he cut a gorge in a southern hill and drained the waters to worship the lotus. Men settled on the bed of the lake and called it the Kathmandu Valley. From then on, the hilltop of the Self-Existent Lord has been a holy place. Later on, Boddhisattva Vajrasatva, covered Swayambhu with a stone slab fearing that its jewels would be stolen by people in the coming Kaliyuga, modern times. Some say that Swayambhu's light was covered in time because few could bear its intensity. Then Santikarcarya, the king who turned into a Bhikchu, monk, raised the first stupa on the holy site.

Though no one is sure how old the stupa is, King Vrisadeva (fifth century AD), the great grandfather of Manadeva I, was well known for his devotion to the stupa. A stone inscription from about that century points out that Swayambhu had been built by that time. In the following years the stupa went through a number of repairs after suffering from lightning, earthquakes, war, and neglect for its upkeep. Reported restorations were done on the stupa during the Licchavi period (300-879), however, the first dated repair is known to have occurred in 1129. Swayambhu was completely destroyed in 1349 when Muslims raided Kathmandu and left most of the Holy shrines in ruins. During the time of King Arjunadeva and his successor, Sthiti Malla, around 1372, the stupa was reconstructed. This time, major modifications to the original structure's form were made to envelop Lord Buddha's power and gave it the basic structure of Swayambhu as we see today, a dome shape achieved with a central beam. Further restorations followed and each project added to the changes of its appearance. The yasti, central wooden beam, the finial surrounding it, and the top parasol needed frequent alterations. The yasti was repaired by Jyotir Malla, and then by his son, Yaksa Malla born in 1408 and died in 1482. In 1565, it was replaced by devotees from the Malla Kingdom of Patan and again after thirty years by Sivasimha (1578-1619), while making an offering. It was broken by lightning fifteen years later and Sivasimha again replaced it. During the time of Laksminarasimha (1621-1641), Sivasimha's heir, Swamarpa Lama coming from Tibet replaced the yasti. Pratap Malla (1641-1674) repaired the whole stupa, and placed a huge vajra mandala, a bronze vajra on a stone mandala, at the top of the stair at the East side. Most of the sculptures at the vicinity of Swayambhu are from the Malla period as the earlier images must have been destroyed during the Muslim raid in the fourteenth century. In 1751 repairs were again started under the supervision of a Tibetan lama, which required 39 kg of gold, 3,500 kg of copper and sponsored was by Jayaprakash Malla and Prithvi Narayan Shah. Other repairs have been recorded in 1808, 1826, and 1928.

Along with the renovation of the Swayambhu, other smaller stupas, chaityas, temples, and rest houses were built around the hilltop. Vrisadeva flattened the top of the hill for the construction of the stupa but left the surrounding trees in their natural state. In the following years, trees were felled and in their place emerged the images of important deities, both Buddhist and Hindu. Around the platform are dharmasalas, secular houses, gonpas, monateries, and five special shrines which are likely to have been made during the transitional period (879-1300). Pratap Malla created a colorful sculpture of Aksobhya at the foot of the eastern slope of the hill and Prithvi Bir Bikram Shah established three similar images on the slope. Pratap Malla also established two tall sikharas dedicating to Vajrayana deities. At the Western side of the stupa is the popular temple of the deity known as Harati to Buddhists and Sitala to Hindus. She is the goddess of protection from smallpox and has many worshippers who pay homage to her at the site. Behind the hilltop is a temple dedicated to Manjusri, or Saraswati-the goddess of learning. Today, statues and shrines dot the stupa complex.

The fifteen meters high Swayambhu has different components to its form and each part has its separate significance. The huge white dome of Swayambhu is known as the anda, the egg, or garbha, womb, which represents the creation of the earth. The dome may enclose the sacred relics but there is no access to the innermost chamber. Also thought to be within the dome are the five Dhyani Buddhas, or Tathagatas. As in other chaityas and stupas around the Valley, the Buddhas are placed in positions at the periphery of the dome. The establishment of Voirachana, the first of the five meditating Buddhas, at the Southeastern side of Swayambhu is rare because Voirachana is traditionally enshrined at the center of the stupa. However, the other four Buddhas, Amitabh, Lord of the West, Amoghsiddhi, Lord of the North, Aksobhya, Lord of the East, and Ratna Sambhava, Lord of the South are facing their expected cardinal directions in their respective positions. Above the dome is the four sided harmika. On each side is painted a face with eyes looking the four directions. The fashion of painting eyes on the harmika was started only in the fifteenth century. It is said that the set of eyes are that of Buddha's below which lies the whole world while others say that they represent the sun and the moon. Above these eyes is a small eye is interpreted as the third eye, signifying the power of the god. Between the eyes is a symbol resembling a question mark, which some perceive as the nose. In actually it is the Nepali symbol for the number "one," which Buddhists intend to represent that there is only one way out of the earthly suffering, Buddhism. Yet others simply know it as unity. Rising above the harmika is the central spire comprised of a thirteen tiered finial, which is made of copper. The finial reflects that there are thirteen obstacles to transcend in order to attain enlightenment and nirvana such as desire, craving, attached, fear, wrath and dishonesty.

Swayambhu is, perhaps, the best place to observe religious harmony in Nepal. The stupa is among the most ancient in this part of the world, and its worshippers are diverse. From Newar nuns, Tibetan monks, and Brahmin priests to lay Buddhist and Hindus, the Lord is supplicated by all. The largest image of the Shakyamuni Buddha in Nepal is in a monastery next to Swayambhu. Other monasteries here have huge prayer wheels, fine Buddhist paintings, and special butter lamps which may be lit after presenting monetary offerings.

Swayambhu is a major landmark of the Valley resting below Nagrjun Hill. It provides and excellent view of the Kathmandu Valley. Devotees have climbed the steps on the Eastern side for centuries, which is verified by the grooves formed by the feet of countless devotees on the stone steps. Great statues of Buddha, stupas and other religious monuments, as well as monkeys scampering in shadows of tall trees, giving the temple the common nickname of "Monkey Temple" among foreign visitors, make the steep climb worthwhile. Although similar in design to its larger counterpart, Boudha, Swayambhu has a flat top to its dome, whereas, Boudha's is rounded. Modern conveniences allow for disabled persons and those pressed for time to reach the stupa via the Western road that runs near to the base of the Swayambhu.