Pancharatra has likely roots in 3rd-century BCE, as a religious movement around the ideas of a sage Narayana who is an avatar of Vishnu.
The earliest use of the word Pancharatra is found in section 7.1.10 of the Taittiriya Samhita, a Vedic text. The section describes a person going through a Pancharatra ritual to become a master of rhetorics. The section 13.6 of the Śatapatha Brāhmaṇa mentions Nārāyaṇa as the primordial divinity who performs this offering. The Narayaniya section of the Mahabharata (XII, 335-351) refers to seven rishis who say the Pancharatra ritual was made consistent with the Vedas. Though the five day ritual is mentioned along with many other sacrifices in the Vedic text, the origins of Pancaratra devotees of Vishnu and their tradition is unclear. The movement merged with the ancient Bhagavata tradition also around Krishna-Vasudeva, and contributed to the development of Vaishnavism.
According to J. A. B. van Buitenen, the word "Pancharatra" is explained in Naradiya Samhita as referring to a tradition of "five knowledges". Similarly, Jan Gonda states that the term "nights" in "five nights" in the Pancharatra tradition may be a metaphor for inner darkness, and "came to mean – how, we do not know", though indeed there have been many interpretations such as "five systems", "five studies" and "five rituals".
The 1st-century works by Shandilya are the earliest known systematization of the Pancharatra doctrine. This doctrine was known and influential around then, as is attested by the 2nd-century CE inscriptions in South India. Evidence suggests that they co-existed with the Bhagavata tradition in ancient times.
The Advaita Vedanta scholars, such as Adi Shankara, criticized elements of the Pancharatra doctrine along with other theistic approaches stating it was against monastic spiritual pursuits and non-Vedic. According to Suthren Hirst, Shankara supported the use of icons and temple worship if it focussed as a means to comprehend Brahman as the sole metaphysical reality. However, he opposed devotional theism as an end in itself and the goal of spiritual pursuits. The Pancharatra tradition has historically disagreed with claims of it being non-Vedic, states Gonda, and Pancharatra texts explicitly state that, "Pancharatra is Vedic, it originates in the Sruti" and that the "Pancharatra precepts and practices should be observed by anyone who has allegiance to the Vedas".
The 11th-century Ramanuja, the influential Sri Vaishnavism scholar, was born in Pancharatra tradition, disagreed with Shankara, and developed a qualified monism doctrine which integrated ideas of Pancharatra movement and those of monistic ideas in the Vedas. Ramanuja stated that the Vishnu of Pancharatra is identical to Vedanta's Brahman, where Purusha reflects the eternal soul that is Vishnu, and Prakriti the impermanent ever changing body of Vishnu.
Vishnu worshipers of today, represented in a wide spectrum of traditions, generally follow the system of Pancharatra worship. The concept of Naḍa and Naḍa-Brahman appear already in Sāttvata Samhita or Sāttvata Tantra and in Jayākhya Samhita, two texts considered most canonical of Pancharatra texts.
Ānanda Tīrtha the founder of Madhva line has written in his commentary on Mundaka Upanishad:
"In Dvāpara-yuga, Vishnu is exclusively worshiped according to the principles of the Pancharatra Scripture, but in this age of Kali-yuga, the Supreme Lord Hari is worshiped only by the chanting of his Holy Name."
Jiva Gosvami had stated in his Paramātma Sandārbha, forming part of six principal Sandārbhas, or philosophical treatises of Gaudiya Vaishnavism, that, "Seeing that the imperfect scriptures in the modes of passion and ignorance bring only a host of troubles, and also seeing that the original Vedas are very difficult to follow properly, and thus being very dissatisfied with both of these, the all-knowing scripture authors affirm the superiority of the Pancharatras, which describe the pure absolute truth, Narayana, and the worship of the Lord, which is very easy to perform."