Michael Fallon said the figure was "highly approximate", partly because there were no UK troops on the ground to confirm the impact of the campaign.
He also said ministers did not believe the action - which began in Iraq a year ago - had caused civilian casualties.
He was responding to a parliamentary question from Green MP Caroline Lucas.
Two years ago MPs rejected possible UK military action in Syria, but in September 2014 approved British participation in air strikes against IS targets in Iraq only.
Ms Lucas specifically asked Mr Fallon what estimate the global coalition to counter IS - made up of more than 60 countries - has made of civilian casualties arising from its activities.
However, he only gave an assessment on the impact of UK action between September 2014 and 31 August this year, adding that "any overall estimates would be a matter for the coalition".
The government is expected to draw up proposals within the next few weeks for missile attacks in Syria against IS.
In August, two British Islamic State jihadists - Cardiff-born Reyaad Khan, 21, and Ruhul Amin, from Aberdeen - were killed by an RAF drone strike in Raqqa, Syria.
The "act of self defence" was lawful, despite MPs previously ruling out UK military action in Syria, the prime minister said, as Khan had been plotting "barbaric" attacks on UK soil.
But Labour leader Jeremy Corbyn said the drone attacks were "legally questionable" and called for a "rapid political development" as a way to end the violence in Syria.
He is expected to oppose any proposal to expand the air campaign against IS.
About 330 fighters from the Islamic State group are estimated to have been killed as a result of RAF air strikes, the defence secretary has said.