He was taken by air ambulance to hospital following the blast but later died from his injuries.
The site in Swains Lane is being redeveloped by Noble House.
A 1920s row of shops is being demolished with plans to replace them with a new residential and retail scheme.
The BBC also reported that the site once contained a petrol station requiring the removal of underground tanks as part of the demolition work.
Highgate councillor and Green London Assembly Member Sian Berry told the BBC: “It’s absolutely shocking. I was there last Friday and saw a big tank that used to store petrol. The first stage of construction was taking these tanks away.”
A spokesman for the Metropolitan Police said: “We were called just after 2pm to reports of an explosion at an address in Swain’s Lane, N6.
“London’s air ambulance attended and took a man aged in his 50s to an east London hospital. Unfortunately he has since passed away. His next of kin have been made aware.
“There have been no arrests and inquiries continue.”