The milestone was reached just a little over 10 years after the service, which is now operated on a daily basis, was launched in 2007.
Raymond and Margaret Henderson were surprised at the airport by Emirates staff celebrating the event and who gave them two return tickets to Dubai.
Emirates vice president UK and Ireland Laurie Berryman said: “We’re honoured to celebrate our two millionth passenger in Newcastle.
"It seems like just yesterday we were welcoming our first passengers arriving from Dubai to Newcastle on a glorious sunny day and hosting football legends Sir Bobby Robson and Alan Shearer at a gala dinner headlined by Chris Rea.
"We hope Raymond and Margaret enjoy a trip of a lifetime to Dubai.
Newcastle airport chief executive Nick Jones added: “Having Emirates fly from Newcastle has brought the people living in the North East closer to the rest of the world.
"The Middle East, Dubai, Asia and Australasia are key travel destinations and export routes for the residents and businesses of Newcastle and the North-East of England."
The daily Newcastle to Emirates is operated by a two-class Boeing 777, departing at 13:00 and arriving in Dubai at 00.15 the next morning.
Emirates currently operates out of six UK gateways, including include London Heathrow, London Gatwick, Birmingham, Newcastle, Manchester and Glasgow.
An extra daily flight will be added from London Stansted as of June 2018, bringing the total of daily flights from the UK to Dubai to eighteen.