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Malta was founded in 1855, under the name of Milton. Shortly afterwards, the name was changed to Etna, then Malta after the Galena Railway station that served the village. The present name is after the island of Malta.

Malta was the site of the first “seedling mile” of concrete pavement for the transcontinental Lincoln Highway in 1914. This short stretch of road in front of the Malta cemetery was one of a number of such seedling miles built to demonstrate construction techniques and generate support for the highway.

Malta struggled financially until the end of World War I, when an influx of new residents to the area arrived. Currently, Malta is a farming community. It also contains Kishwaukee College, founded in 1968.