Wales has been allocated an extra pound;45 million in 2006-7 and 2007-8 for public services such as education, for which the National Assembly has devolved responsibility. In England, the extra cash is going straight to schools, giving pound;190,000, up from pound;98,000, to the average secondary school.
Mr Brown has also announced that he will eventually raise spending per pupil in state schools from pound;5,000 a pupil to exceed the pound;8,000 a pupil average in private schools.
However, the National Union of Teachers Cymru fears Welsh schools' share of the extra cash could be "siphoned off" at either Assembly or local government level in Wales, where less money is ringfenced to schools.
Gethin Lewis, NUT Cymru secretary, said: "We shall be seeking early talks to make sure schools in Wales get their rightful share.
"It does devolution no good if schools feel like poor relations to those over the border."
The Assembly government said ministers would go through normal procedures in considering how to allocate the money.
But there was no mention of schools in its response to the budget, with the focus on extra benefits for working families, lone families and police support services.
An Assembly spokesperson said: "The measures will help develop skills and provide real help to families and the elderly."
But the Welsh Conservatives said education was the top priority of the Chancellor's budget and the Assembly should honour his commitment to schools.