Mr Farthing, who founded animal charity Nowzad after serving in Afghanistan, has been campaigning to get his staff as well as his dogs and cats out of the country.
Sky News reported that a charter plane had arrived in Kabul to collect the ex-Royal Marine commando and his rescue animals.
On Friday, the Ministry of Defence (MoD) announced Mr Farthing and his animals were through airport security.
In a tweet, the MoD said: "Pen Farthing and his pets were assisted through the system at Kabul airport by the UK Armed Forces.
"They are currently being supported while he awaits transportation.
"On the direction of the Defence Secretary, clearance for their charter flight has been sponsored by the UK Government."
Since the collapse of the Afghan government, Mr Farthing and his supporters have campaigned to have his staff and their families, around 68 people, as well as 140 dogs and 60 cats evacuated from the country in a plan he has dubbed Operation Ark.
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