There he also became a PhD in physics (Thesis: "On Resonant Secondary Emission in Sodium Nitrite and Anthracene") in 1981.

In 2006 Jaak Aaviksoo announced that he would be leaving the post of rector of University of Tartu to run for a seat in the Estonian parliament Riigikogu in the 2007 elections as a member of liberal conservative Union of Pro Patria and Res Publica.

Before joining the party and leaving his post as rector, Aaviksoo was considered as a candidate for the presidential elections in 2006, which were won by Toomas Hendrik Ilves.

After already having joined Union of Pro Patria and Res Publica, Aaviksoo sought to become the party's leader for the 2007 parliamentary elections and so candidate for Prime Minister of Estonia, but lost a closely contested duel within the party to internationally renowned two-time former Prime Minister Mart Laar.

Having assumed office on 5 April 2007, his first primary goals as Minister of Defence were restructuring the power management of the Estonian Defense Forces and dealing with the situation of the Bronze Soldier of Tallinn, a Soviet war monument, which was moved to a cemetery, causing much controversy and ethnic tension between a large proportion Estonians and local Russians.

Since September 2015 Jaak Aaviksoo is the rector of Tallinn University of Technology (TalTech).