Many of the 843 pieces were stolen during Afghanistan’s civil war in the 1990s and ended up on the black market.
Some of the items, which include stone statues of Buddha and intricate ivory carvings, are up to 4,000 years old.
The British Museum in London has helped to complete their return.
Some of the stolen artefacts were recovered by British border forces and police, while others were found in private collections and bought back by generous donors.
One stone Buddha, thought to be around 1,800 years old, was stolen from the museum in Kabul and recovered in Japan.
The British Ministry of Defence flew the pieces back to Afghanistan in large crates, landing at their military base in Camp Bastion.
Afghan archaeologists say the repatriation of the treasures, which had been feared lost forever, is a source of national pride.
More than two thirds of the exhibits at the National Museum in Kabul were stolen or destroyed during the civil war.
The BBC’s correspondent in Kabul, Aleem Maqbool, says there will be concerns about the fate of the artefacts, given the unpredictability surrounding Afghanistan’s future.
But archaeologists here say having so many of their treasures back on home soil is a source of great national pride, our correspondent adds