The Letterkenny Rovers boss has been in the position for the past 14 years.
It had been speculated in recent weeks that McConigley was unhappy with certain aspects of the league and was ready to step down.
A statement released earlier confirmed the Fanad man had stepped down.
“It is with great regret that the Ulster Senior League confirm the departure of Eamonn McConigley from the role of chairman.
“Eamonn has submitted his resignation with immediate effect to the league secretary (Mark Duffy).
“The Ulster Senior League Executive would like to thank Eamonn for his dedication and services to the league and football over the 14 years he held the position and wish him well for the future.
“We know that he will continue to support the league in his role as manager of Letterkenny Rovers FC.”