The 28-tonne "battle bus" is thought to have been built in the 1980s for the then Prime Minister's Northern Ireland tour.
The vehicle went under the hammer on Thursday night and beat the estimate of £10,000, selling for a final £16,940 to a vehicle collector.
"There was immense interest in the bus," Jonathan Humbert from Northamptonshire-based JP Humbert Auctioneers said.
"It sold to a spontaneous round of applause in the saleroom."
"This isn't a good-looking vehicle by any stretch of the imagination - but it is of social and historical interest," said Mr Humbert previously.
"It is an irreplaceable one-off, an iron bus for the Iron Lady."
The bus has a blast-proof floor and armour-plated glass throughout, as well as a bomb-proof armour-plated body. It has 17,398 miles on the clock.
It was thought to be chemical, biological and nuclear-proof - once having its own auxiliary generator and air supply.
Due to the high security surrounding the visit, the auctioneer could not confirm if Mrs Thatcher used the vehicle but said it was later used to move military troops in the region.
The bus boasts a Foden chassis, a body by Glover and Webb and is powered by a 12-litre Rolls-Royce engine.
Mr Humbert said the bus, which has room for around 35 passengers, had come from a private vendor who bought it from a research and development company which in turn bought it from the government.