The Balfarg henge was excavated between 1977 and 1978 by Roger Mercer prior to the development of a new housing estate, work which established that the two extant standing stones were part of a circle that stood within the henge. The two surviving specimens lined the north-west oriented entrance to the henge. Mercer's report is available online.
Within the 64.9m diameter henge were found broken Neolithic pottery, burnt wood and bone which had been dumped on the site prior to the erection of a 25m wide timber circle of 16 wooden posts. Two especially large portal timbers stood on the west side of the circle. It is likely that the henge was built after these phases of activity. Grooved ware pottery found in the postholes dates to around 2900 BC. Some of the vessels may have been used to hold black henbane (Hyoscyamus niger) which is a poison but also a powerful hallucinogen. This discovery is briefly explored in the journal Antiquity in the article 'The use of henbane as a hallucinogen at Neolithic 'ritual' sites: a re-evaluation.'
Five further concentric post rings had also been erected outside and inside the main wooden circle although these were made from narrower timbers and may have supported hurdling or a palisade.
Later during the site's use the timber circle was replaced by two concentric stone circles, again with an entrance to the west and some time after this the henge was constructed. Around 1900 BC a pit was dug in the centre of the stone circles and in it was placed the body of a young man along with a flint knife and a handled beaker.
Later excavation between 1983 and 1985 by Barclay and Russell-White demonstrated that there were scatters of earlier Neolithic pits round the Balfarg henge. These excavations also discovered a second henge, which surrounded a Neolithic timber mortuary enclosure. A second such timber structure lay just outside the henge, partly overlain by a complex of two burial cairns.
Nearby is the Balbirnie stone circle, which is also part of the complex.