In 1918 Jaakson organised a paramilitary defense group, the Estonian Defence League, in Türi. At the start of the Estonian War of Independence on 28 November, he joined the 6th infantry regiment, serving first as a company commander, and from 28 December as the commander of the 2nd battalion. He fought against both the Red Army and the "Baltische Landeswehr", and suffered a concussion in June 1919 near Stalbe in Latvia. In October Jaakson was promoted to the rank of captain. For his service in the War of Independence Jaakson was awarded Estonia's Cross of Liberty and Latvia's Order of Lāčplēsis, as well as a farm and 50,000 marks.