In a statement from EWEA, Kjaer said he would be moving on to "something new and currently undefined". He will have been in the CEO role for seven years by the time he leaves.
Kjaer added: "This is entirely my own decision and the rather long notice is motivated only by my intention to ensure that the EWEA Board and staff can prepare the transition in an orderly and timely fashion."
EWEA said it hopes to announce an replacement by the end of the year.
EWEA president Arthouros Zervos said: "Kjaer has transformed EWEA from a small association to probably the most respected renewable energy association in the world, and one of the most respected associations of any kind in Brussels.
"He has insisted on the highest standards which are reflected in everything that EWEA stands for - credible research, informative publications, strong communications, effective advocacy and top quality events. He is a hard act to follow, but leaves his successor a flourishing association with an excellent secretariat."