He told a meeting of Catholic principals in Cookstown there was no room for "splendid isolation".
Twenty-eight Catholic grammar schools have set transfer tests as part of the Post-Primary Transfer Consortium.
That is despite the position of the Catholic church which says it wants an end to academic selection.
Cardinal Brady said that there should be no such thing as a second class Catholic school.
But he said pressure applied on principals would be "gentle".
He added: "I think they will do what is the honourable and right thing but it takes time. I would appeal for patience.
"The views of parents come into this too. There are parents who intend on having grammar school education."
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SIC: BBC