Britain pulled out of the country in secret on June 24 with flag lowering services held behind closed doors for operational security.
On Thursday, Johnson made the announcement to the House of Commons that all British troops assigned to the NATO mission were returning home.
"I can tell the house that most of our personnel have already left," Johnson said in the statement.
Over 150,000 British troops have served in the conflict.
"I hope that no-one will leap to the false conclusion that the withdrawal of our forces somehow means the end of Britain's commitment to Afghanistan," Johnson said.
The move comes as Iran has offered to host peace talks between the Afghanistan government and the Taliban.
The country will provide $137 million in funding for the Afghanistan government this year.
The country's remaining 750 troops are leaving Afghanistan. The United States still has 2,500 soldiers in Afghanistan. Britain has lost 457 troops over the course of their involvement in the war sprawling over the course of two decades.
Carter said 50% of rural territory is held by Taliban forces.
The withdrawal comes as the United States recently announced a 90% withdrawal in Afghanistan in the longest war in that nation's history.