Nicky Morgan pointed to partnership working with more successful schools as the way for struggling primaries to improve their performance.
The latest primary school league tables show that despite improvements there are schools in the region where fewer than half of 11-year-olds go on to secondary school without reaching the expected standard.
Mrs Morgan said: “As I go across the country I meet heads and teachers who are passionate about improving, about doing the best by their students.
“What the Department for Education, regional schools commissioners, local authorites can do is to encourage really excellent heads and teachers in nearby schools and colleges to spread their expertise.
“I would just say to heads and teachers, if you are in schools where there are difficulties please be open and receptive to help from outside, from nearby heads many of whom have gone through the issues they are going through now and who are willing and wanting to work with those schools to make sure all our students go to a good local school which is what I want.”
Chancellor George Osborne set aside £10 million in his Autumn Statement last week to help academy chains take over the management of more schools as part of efforts to drive up standards in the North.
Mrs Morgan said the money would help “encourage those who are in need of improvement to become academies”, a move which sees schools leave local authority control with the support of a sponsoring organisation.
The Education Secretary said: “I believe passionately in the autonomy of the heads. I think the heads are best placed and teachers are best placed to make decisions for students in their schools.
“I also believe that sponsored academies do incredibly well and again the Ofsted results showed that yesterday.”
The Education Secretary was speaking during a visit to St Margaret’s Church of England Primary School, in Horsforth, Leeds, yesterday where she watched lessons in action as well as speaking to staff and pupils.
Nationally, the number of primaries failing to get 11-year-olds to the expected standards in the three Rs has remained static this year, despite schools facing tougher government targets.
Overall, 768 schools failed to meet the ‘floor standard ‘this year, compared with 767 last year
The percentage of children achieving the expected level in reading, writing and maths rose by three percentage points to 79 per cent.
Shadow Education Secretary Tristram Hunt said: “It is very encouraging to see that primary schools are continuing to make progress, in line with the steady improvements made over the past twenty years.
“But under David Cameron’s Government we have a schools policy that puts these gains at risk. His Government has signed off on allowing unqualified teachers to work in our classrooms on a permanent basis. For three consecutive years teacher recruitment targets have being missed.
“We have big challenges in our school system, not least that 170,000 pupils are now in inadequate secondary schools.”
The latest primary school league tables were published just a day after watchdog Ofsted revealed that pupils in Yorkshire are less likely to go to a good secondary school than anywhere else in the country.
According to Ofsted, one third of pupils in the region go to schools which its inspectors have decided to do not meet the required standard.
In some areas of Yorkshire that figure rises to more than half.
The chief inspector of schools, Sir Michael Wilshaw, has suggested that while primary schools continue to get better, improvement in secondary schools across the country has stalled.