Fahlenius was born on 30 October 1674 in Falun in the Swedish Empire, the son of a priest and teacher Niklas Håkansson Fahlenius and his wife Brita Jonasdotter Fahlberg.
After basic education at Falun Trivial School, in 1695 he commenced studies at Uppsala University from where he graduated with his Masters in 1707.
On 18 March 1734 he was appointed Bishop of Turku and was consecrated some time later that year by Archbishop Johannes Steuchius.
One of his daughters was the mother of Abraham Niclas Edelcrantz, poet and inventor.
Fahlenius is buried in Turku Cathedral along with his second wife and two of their children.