Flag-waving Estonians watched the parade in capital Tallin, with about 11,000 soldiers and hundreds of vehicles from both the domestic army and other NATO countries taking part in a show of strength.
Along with fellow Baltic states Latvia and Lithuania, Estonia declared independence in 1918 as the Tsarist Russian empire collapsed during World War I.
But it was annexed by the Soviet Union under a 1939 deal with Nazi Germany in World War II.
The nation of 1.3 million people then broke free from the crumbling Soviet Union in 1991.
"The independence and freedom of our people has never been and should not be taken for granted," General Riho Teras, Estonia's chief of staff, said at the parade.
"The war of independence sent a clear message: anything is possible if a nation really wants it," he said, referring to the 1918-1920 war with the Russian empire.
Tensions with Russia remain, and the largely secular country joined NATO and the European Union in 2004.
Relations have been particularly strained by Moscow's 2014 annexation of Crimea from Ukraine and the ongoing conflict in eastern Ukraine between pro-Russia rebels and the government.
Festivities to mark the centenary will run until 2020 and include concerts and exhibitions.
Estonia announced Thursday that US President Donald Trump will welcome his Estonian, Lithuanian and Latvian counterparts in Washington on April 3 to discuss security and economic ties.
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