"I am not leaving Congress because I have lost my heart for service -- to the contrary, I see a new way to serve," Emerson said in a statement. "I did not go seeking this opportunity, but I am excited about the new challenge it offers to find ways to promote strong rural policy."
Emerson's resignation is effective in February.
She will be president and chief executive officer of the association.
The 8th Congressional District is a safe Republican district, Roll Call reported.
State Republicans said the two main contenders are Lt. Gov. Peter Kinder and Lloyd Smith, executive director of the state GOP.
Emerson was elected to Congress in a 1996 special election, succeeding her late husband, GOP Rep. Bill Emerson. After winning only 50 percent of the vote in her first general election, Emerson was returned to Congress by larger margins of the popular vote. Last month, she won with 72 percent.