Lehner, who acknowledged he would be affected by his own decision, ordered the state to raise judicial pay to reflect cost of living increases since 1998.
He was ruling on a lawsuit brought by four judges. Chief Judge Judith Kaye is leading a different lawsuit against the Legislature to secure raises - but has warned judges not to protest through action from the bench.
New York's highest-paid state judge makes $156,000 a year.
Lehner said previously that judges' pay has been so ravaged by inflation in the last nine years that a first-year associate at a large New York City law firm would have to take a pay cut to become the state's chief judge.