Murgenthal is first mentioned in 1255 as "Murgatun". The "Herrschaft" rights to the village belonged to the Counts of Frohburg until 1299, when they went to the Habsburgs. From the Bernese conquest of the Aargau in 1415, until 1798, the rights were held by city of Bern. Between 1640-45 the Governor of Aarburg, Jacob Wyss, build the "Rotkanal" (Red Canal) which transported water from the head waters of the Murg river to the meadows at Rothrist. Between 1798-1802 it was part of the Canton of Bern. Since 1803 it belongs to the canton of Aargau. Until 1900 the village of Murgenthal was part of the municipality of Riken. In 1901 the municipality of Riken joined the municipality of Balzenwil to form the new municipality of Murgenthal.