Yoga philosophy is one of the six major important schools of Hindu philosophy, though it is only at the end of the first millennium CE that Yoga is mentioned as a separate school of thought in Indian texts, distinct from Samkhya. Ancient, medieval and modern literature often simply call Yoga philosophy Yoga. A systematic collection of ideas of Yoga is found in the Yoga Sutras of Patanjali, a key text of Yoga which has influenced all other schools of Indian philosophy.

The metaphysics of Yoga is Samkhya's dualism, in which the universe is conceptualized as composed of two realities: Puruṣa (witness-consciousness) and Prakṛti (nature). Jiva (a living being) is considered as a state in which puruṣa is bonded to Prakṛti in some form, in various permutations and combinations of various elements, senses, feelings, activity and mind. During the state of imbalance or ignorance, one or more constituents overwhelm the others, creating a form of bondage. The end of this bondage is called liberation, or mokṣa, by both the Yoga and Samkhya schools of Hinduism, and can be attained by insight and self-restraint.

The ethical theory of Yoga philosophy is based on Yamas and Niyama, as well as elements of the Guṇa theory of Samkhya. The epistemology of Yoga philosophy, like the Sāmkhya school, relies on three of six Pramanas as the means of gaining reliable knowledge. These include Pratyakṣa (perception), Anumāṇa (inference) and Sabda (Āptavacana, word/testimony of reliable sources). Yoga philosophy differs from the closely related non-theistic/atheistic Samkhya school by incorporating the concept of a "personal, yet essentially inactive, deity" or "personal god" (Ishvara).

Yoga as a separate school of thought is mentioned in Indian texts from the end of the 1st millennium CE. A collection of practices and some ideas of the Yoga school of Hinduism is found in the Yoga Sutras of Patanjali. After its circulation in the first half of the 1st millennium CE, many Indian scholars reviewed it, then published their Bhāṣya (notes and commentary) on it. The commentary by Vyasa may have been written by Patanjali himself, forming an integrated text called the Pātañjalayogaśāstra ("The Treatise on Yoga of Patañjali"). Yoga as a separate school of philosophy has been included as one of the six orthodox schools in medieval era Indian texts; the other schools are Samkhya, Nyaya, Vaisheshika, Mimamsa and Vedanta. According to Bryant,

Sāṁkhya and Yoga should not be considered different schools until a very late date: the first reference to Yoga itself as a distinct school seems to be in the writings of Śaṅkara in the 9th century C.E.

There are numerous parallels in the concepts in the Samkhya school of Hinduism, Yoga and various strands of Buddhism, particularly from the 2nd century BCE to the 1st century AD, notes Larson. From the Samkhya school of Hinduism, the Yoga Sutras adopt the "reflective discernment" (adhyavasaya) of prakrti and purusa (dualism), its metaphysical rationalism, as well its three epistemic methods to gaining reliable knowledge. From the Buddhist practice of nirodhasamadhi, argues Larson, the Yoga Sutras adopt the pursuit of an altered state of awareness, but unlike Buddhism, which believes that there is no fixed self, Yoga is physicalist like Samkhya in believing that each individual has a self and soul. The third concept that the Yoga Sutras synthesize into its philosophy is the ancient ascetic traditions of isolation, meditation and introspection.

Yoga-philosophy is Samkhya. In both, the foundational concepts include two realities: Purusha and Prakriti. The Purusha is defined as that reality which is pure consciousness and is untouched by thoughts or qualities. The Prakriti is the empirical, phenomenal reality which includes matter and also mind, sensory organs and the sense of identity (self, soul). A living being is held in both schools to be the union of matter and mind. The Yoga school differs from the Samkhya school in its views on the ontology of Purusha, on axiology and on soteriology.

The metaphysics of Yoga-Samkhya is a form of dualism. It considers consciousness and matter, self/soul and body as two different realities.