The flights returned to RAF Brize Norton in 2011 when it was announced that RAF Lyneham would close.
Repatriations were switched from Brize Norton to RAF Lyneham in 2007, meaning public ceremonies were held at nearby Wootton Bassett.
The Hercules transporter planes, which were the heart of RAF Lyneham, left last year for RAF Brize Norton in Oxfordshire.
BBC: RAF Lyneham: MoD reveals details of training centre plan
Many of the 4, 500 military and civilian personnel have since moved to Brize Norton, with only 15 still based in Lyneham.
BBC: RAF Lyneham: MoD reveals details of training centre plan
The XH558 has been based at South Yorkshire's Robin Hood Airport since March 2011 after the RAF Lyneham base closure was announced.
The bodies of the two were flown into RAF Lyneham in Wiltshire and then passed through the nearby town of Wootton Bassett.
As his body arrived at RAF Lyneham on Thursday, his family said he would be laid to rest beside his baby daughter.
The decision to close RAF Lyneham was made by the MoD in 2002 as part of a strategic review of military bases.
More details have been revealed about Ministry of Defence (MoD) plans to turn RAF Lyneham in Wiltshire into a defence training centre.
BBC: RAF Lyneham: MoD reveals details of training centre plan
His coffin was flown into RAF Lyneham and hundreds of people gathered in the Wiltshire town of Wootton Bassett to see it driven through.
Its future was put in doubt after the government announced last year that RAF Lyneham in Wiltshire would open a training college in 2013.
The MoD made the decision to close RAF Lyneham in 2002.
BBC: RAF Lyneham: MoD reveals details of training centre plan
The first repatriation service took place in the town in April 2007 when the bodies of military personnel began arriving at the nearby RAF base at Lyneham.
The last repatriation took place in August as RAF Lyneham ceased to operate as a flying base on 30 September, and is due to close on 31 December 2012.
Training in maintaining machinery and military equipment which currently takes place at Bordon, in Hampshire, and Arborfield, in Berkshire, will be transferred to the new college at Lyneham in 2015.
BBC: RAF Lyneham: MoD reveals details of training centre plan
Locals have turned out to honour the corteges of more than 100 service personnel killed in Iraq and Afghanistan, as they made their way from nearby RAF Lyneham to a morgue in Oxford.
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