Menziken is first mentioned in 1045 as Manzinchouen though that comes from a 14th Century copy of the original document. In 1295 it was mentioned as Menzchon. However, the current site of Menziken was settled earlier. Both Roman era ruins and Alamanni graves have been discovered in the municipality. During the High Middle Ages it was owned by the Counts of Lenzburg. In 1173 it passed over to the Kyburgs and following the extinction of the Kyburg line, in 1273 it passed to the Habsburgs. The Habsburgs held the rights to high justice while their vassals, the Lords of Reinach, held the rights to low justice. From the conquest of Aargau in 1415 until the creation of the Helvetic Republic in 1798, the village was under Bernese domination. At that time, Menziken belonged to the district (German: Oberamt) of Lenzburg. With the creation of the Canton of Aargau through the Act of Mediation in 1803, Menziken became a municipality in the new canton.
During the Middle Ages Menziken was part of the Catholic parish of Pfeffikon. Following the introduction of the Protestant Reformation in 1528, it was initially part of Gontenschwil parish and then of the parish of Reinach. It became the independent parish of Menziken-Burg in 1889-90, with the construction of its own church. The Catholic Menziken-Reinach Diaspora parish was created in 1906-07 when St Anne's Church was built in the municipality.
In 1729 a cotton factory was built in the municipality. This factory was followed by numerous weavers, spinners and dyers, which until the 19th Century provided a major source of income. In 1838 Samuel Weber opened a cigar factory in the village which lead to the cigar industry dominating the entire upper Wynental. The cigar companies represented a major employer until the second half of the 20th Century. Major employers in the early 21st Century include the Schlör AG (which had developed from the brewery founded in 1888 and today produce soft drinks, fruit and apple juice) and Alu Menziken, which produces metal goods. Since 1904 Menziken has been the terminus of the Wynental- und Suhrentalbahn.
Menziken has an area, as of 2009, of 6.39 square kilometers (2.47 sq mi). Of this area, 3.04 square kilometers (1.17 sq mi) or 47.6% is used for agricultural purposes, while 1.49 square kilometers (0.58 sq mi) or 23.3% is forested. Of the rest of the land, 1.87 square kilometers (0.72 sq mi) or 29.3% is settled (buildings or roads), 0.01 km2 (2.5 acres) or 0.2% is either rivers or lakes and 0.01 km2 (2.5 acres) or 0.2% is unproductive land.
Of the built up area, industrial buildings made up 2.8% of the total area while housing and buildings made up 17.1% and transportation infrastructure made up 4.4%. Power and water infrastructure as well as other special developed areas made up 2.7% of the area while parks, green belts and sports fields made up 2.3%. 21.8% of the total land area is heavily forested and 1.6% is covered with orchards or small clusters of trees. Of the agricultural land, 29.9% is used for growing crops and 16.6% is pastures, while 1.1% is used for orchards or vine crops. All the water in the municipality is in rivers and streams.