A small chartered plane landed at Traigh Mhor beach runway on the remote island of Barra with the 14-year-old’s coffin at 12.45pm on Sunday.
Her parents Roddy and Marion were on board.
Eilidh was among 22 people who died in the terrorist attack at the Ariana Grande concert on Monday May 22, which also left dozens injured.
Her friend Laura MacIntyre, a fellow pupil at Castlebay Community School on the island, was also seriously injured in the bombing at Manchester Arena.
The 15-year-old is still in hospital in Manchester.
On arrival of the plane, Fr John Paul MacKinnon performed a blessing over the casket, which was draped in the green and white flag of Barra.
A procession of six firefighters and two other groups of men relayed the coffin, at waist height, 70 yards across the sandy shallow bay to the hearse.
Piper Duncan Nicholson, son of Eilidh’s piping tutor Donald Patrick Nicholson, led the procession with three slow airs she had been learning.
They were Mull of the Mountain, Sine Bhan and Leaving Ireland.
Donald Patrick, 76, who taught her since she was eight years old, said: “She was brilliant, a fantastic girl. It’s devastating.
“I’ve known her since she was in primary school.
“She was absolutely great, brilliant - a fantastic girl. You couldn’t get better.”
When the coffin was lifted into the hearse, Eilidh’s parents and two sisters walked across the beach to follow in a black car.
Her body was taken to the family home in Castlebay.
A crowd of around 50 people were at the airport to observe the ceremony.
They could be seen embracing each other and wiping away tears once the hearse left.
Around two dozen vehicles followed as the family made its way home.
Other members of the community lined the road to pay respects as they passed.
The funeral will take place on Monday June 5 at Church of Our Lady, Star of the Sea in the village.
Scottish Government ministers - including Deputy First Minister John Swinney, Humza Yousaf MSP and Na h-Eileanan an Iar MSP Alasdair Allan - are expected to attend the ceremony.
First Minister Nicola Sturgeon said: “I know that everyone in Scotland will join me in sending our heartfelt sympathy to Eilidh’s family and friends ahead of what will be the most difficult day imaginable.
“Everything that I’ve heard, seen or read about Eilidh shows that she was a vivacious, fun-loving young woman with a bright future ahead of her, and I know that the community on Barra will pay her a fitting tribute. Her family are in my thoughts.”
Businesses on the island are to shut for the whole of Monday or a number of hours as a mark of respect and to allow staff to attend the funeral.
A large procession is anticipated to follow the hearse as it carries Eilidh’s body from the church to Vatersay, an island connected by causeway where she is originally from, for her burial.
Greater Manchester Police Chief Constable Ian Hopkins and Mayor of Greater Manchester Andy Burnham have sent a message and wreath.
Barra’s community has been fundraising for the families of both victims.
Money has been asked to be donated to Cobhair Bharraigh, a local home-based support service and day care centre, which was Eilidh’s favourite charity.