The authority is ranked joint 49th out of 152 nationally for test results in both English and maths – down from 21st last year.
Record results have seen 81 per cent of 11-year-olds achieve the expected level four standard - up from 78 per cent last year.
But the East Riding has slipped down the table because other areas have made greater improvements.
Head of achievement and inclusion and East Riding Council Mike Furbank said: "Some authorities have improved faster than we have. We are trying to improve as rapidly as we can."
Results are better than the national average of 79 per cent, making the East Riding the second-best performing authority in the Yorkshire and Humber region.
The East Riding is continuing to make progress year on year, with 87 per cent gaining the benchmark in English and 85 per cent in maths.
Mr Furbank said improving school performance is against the backdrop of low funding for the East Riding, which is the country's eighth worst funded authority.
He said: "It is particularly heartening to see the improvement in progress measures which every child contributes to and the significant improvement in level five performance which has been a real focus for the East Riding.
"It should be remembered, however, that poor funding impacts on class size and that the resourcing of schools both in staff and physical terms is directly related to our position as eighth worst funded authority.
"East Riding's results remain positive and above the national average despite years of under investment by central government."
Councillor Julie Abraham, portfolio holder for children, young people and local authority schools, said: "We are celebrating the real achievement of this group of children as they progress to East Riding secondary schools as the highest achieving year group ever."