A High Court judge ruled that David Cardoza does not yet have to pay back £180,000 he got from the club in 2015.
The council, which lost £10.25m in a loan for a failed stadium revamp, said it will take the case to trial.
Mr Cardoza told the BBC he had "always acted with honesty and integrity".
"In an ongoing attempt to recover losses, the council continues to incur hundreds of thousands of pounds in costs pursuing proceedings that are destined to fail," he said.
The council's application for immediate summary judgment in respect of the £180,000 - which is only part of a much larger claim -  was dismissed by the court
The council is trying to re-coup more than £3m from Mr Cardoza and his father Anthony in its legal action.
Northamptonshire Police confirmed Mr Cardoza remains on bail while they continue to investigate "alleged financial irregularities" over the loan.
According to his evidence, Mr Cardoza got the money from club because he was "effectively foregoing his salary and instead being repaid the monies which he was owed by the club in respect of his directors' loan account".
Mr Cardoza, who left the football club 16 months ago, said he was pleased by the court's decision.
"The judgment is clear that, even if the council was successful in its claim, the football club would then be indebted to me for the same amount, " he said.
A council spokesman said: "We accept the court's decision however, this matter must now go to trial."
The ex-Northampton Town Football Club chairman has been backed by a court over the latest bid by a council to recover public money it lost in a failed loan.