The airline was forced to apologise after Jack Johnson's family were questioned at Split airport in Croatia on Tuesday.
The youngster was left in tears after staff said they had no record of his disability – despite mum Alex saying she told the airline well in advance.
The family, from Wigan, eventually found out Jet2 had not sent through the details.
The distraught boy was finally allowed to board the plane but only after a "shambolic" and "humiliating" experience.
Jack's mum wrote in her blog: "As a family we need and love our holidays because of the underlying heartbreak we live with every day as we watch our son’s muscles waste away.
"Eventually it will be impossible for us to take Jack on holiday and make the precious memories we cherish with him."
She added: "Incompetence and error at Jet 2 holidays has ruined our holiday.
"I can honestly say we have never experienced anything as shambolic and as humiliating for our son as our flight home from Split with Jet 2.
"I didn’t want us to run into any problems as Jack hates people staring and attention being drawn to him. It’s hard for him being a kid that is different.
"The indignity of the situation was awful. He was crying and saying I just want to go home to my Grandma’s."
Jack – the son of former Wigan Warriors player Andy Johnson – was diagnosed with the incurable Duchenne's Muscular Dystrophy in 2012.
A Jet2 spokesman said: “We are extremely sorry to hear of this experience, and we appreciate that it has been very distressing for Jack and his family."
They added: "We have been in contact to unreservedly apologise for the upset caused, and we would like to reassure Jack, his family, and all our customers, that this is not our normal standard of service.
"Although this is an isolated incident, we have learnt a number of lessons and we are urgently reviewing all our procedures to ensure that this does not happen again.”
Sun Online has contacted Jet2 for comment.
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