The village school received the top grade in 25 out of the 27 areas, with the other two rated good.
Headteacher Martin Alger said: "We are over the moon and absolutely amazed. It has knocked us sideways.
"We know we have outstanding areas but Ofsted altered some of our own self evaluation judgements to outstanding, saying we were being too modest."
He added: "They put the result down to outstanding teaching and learning and outstanding leadership and management.
"The pupils behaviour was described as exemplary, and the curriculum top quality.
"One of the key bits of the inspectors judgement was based on a 30 minute chat with our Year Six pupils who she asked pointed questions, but she said she was overwhelmed by their answers and their understanding by our learning."
Lead inspector Mrs Linda Murphy said: "I judge that Gilberdyke Primary School gives you an excellent education.
"This is not only because the school is led outstandingly well but the quality of teaching is equally as strong. It means you learn at a fast pace and reach high standards."
In the school's last Ofsted inspection four years ago, it received an overall good grade.
"The teachers we have are great and make the curriculum interesting which the children are engaged by," added Mr Alger.
"Parents are also supportive and interested in us doing the best we can."
He revealed that during lessons the pupils are made to do a lot of investigating and problem solving, in order to get them as involved as possible.
Teaching is changing, he added, with teachers' roles now more secondary instead of standing at the front of the classroom.
"We used to talk about the pupils bouncing out of school and the teachers leaving tired, but we are trying to reverse that," said Mr Alger, who has been at Gilberdyke for eight years.