The competition has been running for 23 years and was won this season by Swansea City at the Millenium Stadium.
"This is excellent news and provides a real end-of-season boost for League clubs," said League chairman Lord Mawhinney.
"All supporters want to see their club competing for silverware and the Johnstone's Paint Trophy gives clubs from Leagues One and Two a cup competition that realistically they can win."
A number of Conference clubs have joined teams from Leagues One and Two in the competition in recent seasons.
According to a Football League spokesman, the competition structure for next season is still being considered.