Before January 1, 1914, the county was part of neighboring Fremont County. The newly established county was named for American president James Madison.

BYU Idaho, formerly Ricks College is located here.

Madison County was declared a national disaster area after the Teton Dam flood of June 5, 1976.

Madison County was created from Fremont County by an Enabling Act of the Idaho Legislature on February 18, 1913.  It was the thirty-third county of the state.  At the time of creation, its eastern boundary extended to the Wyoming line and included Teton Valley.  Teton County was created in 1915, leaving Madison with its present boundaries.

Though the legislature had passed the law providing for the creation of Madison County and the governor had signed the bill, the people needed to approve.  An election was held on November 7, 1913 for the people to pass the bill.  All voters in then Fremont County were eligible to vote.  1760 votes were for its creation and 793 against. In Rexburg 793 votes were cast and only seven disapproved.

On November 8, the day after the election, the governor proclaimed the creation of Madison County.  A big celebration was held in Rexburg.  A program was held in the Tabernacle and over five thousand people attended.  A big barbecue was served consisting of two steers, six pigs, six lambs, and two thousand loaves of bread.

Governor Haines appointed the first officials of Madison County on November 14.  Officials named were:  John Taylor of Sunnydell, J.K. Orme of Sugar City, and R.G. Meikle  of Clawson, County Commissioners;  John Hegsted, auditor and recorder; Conrad Walz, assessor, Harry Randall, treasurer;  Oliver C.Dalby, county attorney; I.N. Corey, sheriff;  L.T. Perry as county school superintendent; and  Ed W. Stacy was coroner.  These men entered into their duties on January 5, 1914.

The first offices were leased in the old Webster – Winter building on East Main (upstairs above the Subway and Community Care).  The old dance hall in the building was made into a court room and public and private offices, and a jail of four cells was built at the rear of the building.

The courthouse we have today was finished in December, 1920.