Carolyn Mugar, who guided the organization since 1985 as it raised $80 million to support family farmers, will continue on as an advisor.
The Texas icon led a day-long celebration in support of America’s family farmers.
Farm Aid will be held in Saratoga Springs, New York, on Sept. 21.
The unannounced set by Dylan helped close the event held to benefit family farmers.
In July 1985, the singer's remark onstage at the Live Aid charity mega-concert inspired Nelson to create his first benefit for America's family farmers in September of that year.
Dave Matthews and Tim Reynolds, Margo Price and Bob Weir will also be on Sept. 23 bill.
John Mellencamp, co-founder of Farm Aid, sang Tuesday for those gathered before they marched up Pennsylvania Avenue to the U.S. Capitol building.