The guidance, expected to be published shortly by the Department for Education and Skills, says that schools may find it difficult to introduce the charges but that they are necessary to keep the activities going in the long-run.
Many schools already charge for some out-of-lesson services, but the practice varies.
The guidance is part of the Government's drive to make all schools offer extended activities such as childcare and homework clubs from 8am to 6pm, by 2010. The DfES has spent pound;160 million on the project and plans to spend a further pound;680m over the next two years, but says the services need to become self-funding.
The guidance tells schools: "You may charge for some study support activities, such as sports coaching or dance classes, but not for offers relating directly to a child's attainment, such as targeted literacy support."
It adds that schools might still be able to fund or subsidise parenting classes and breakfast clubs if they can argue that they help educational achievement.
Schools which already charge for after-school clubs and are mentioned in the guidance include Kingsdown high school in Wigan, which charges pound;7 a session, and Delaware primary in Cornwall which charges pound;1.50.
But some extended schools which have avoided charging said they would resist the measures. Kenny Frederick, head of George Green school in Greenwich, said introducing payments would be "unworkable" and would undermine work with the community.
A key reason why schools may have to charge for extended services is to pay staff, as it may otherwise be difficult to find teachers who will run them.
The NASUWT, Britain's second-largest teachers' union, has won a guarantee from ministers that extended schools will not lead to longer hours for teachers.