He had been barred on Friday from entering Russia via a Moscow Airport, having to use land transport through Kiev to reach the peninsula, which declared its independence from Ukraine to join Russia in March.
Welcomed by thousands of Crimean Tatars who were expecting him to come in, Kirimoglu failed to go in through the checkpoint, saying he would return to the Ukrainian capital.
Kirimoglu urged for calm among his supporters, calling on them to continue a non-violent struggle against the 'existing regime.'
Earlier on Saturday, Crimea's Tatar National Assembly called off religious spring celebrations set in a few days' time to protest Kirimoglu's being denied entry.
On the Ukrainian border leading to the peninsula, Kirimoglu reportedly tried to go in but was stonewalled by Russian soldiers.
In late April, Russian officials had reassured Kirimoglu he was freed to enter Russia, despite rumors to the contrary.
At the border on Saturday, Russian troops fired into the air, not letting thousands of Crimean Tatars - including President of the National Assembly, Rifat Cubarov and Crimean Deputy Prime Minister, Lenur Islamov - pass the Armyansk checkpoint.
Tatars climbing over the roadblocks met Kirimoglu in a buffer zone after he passed the checkpoint on the Ukrainian side. Upon this incident, Russian soldiers reportedly called for back-up and closed the border gate.
On March 21, Russian President Vladimir Putin signed into law the annexation of Ukraine's strategic peninsula of Crimea. The move followed a March 16 referendum in Crimea where around 97% of voters chose to secede from Ukraine and join Russia. The United States, the European Union and Ukraine regard the vote as "illegitimate."
On April 21, Putin signed a decree to rehabilitate Crimean Tatars and minorities, pledging to restore their rights and freedoms. Two days later, Kirimoglu claimed he was forced by unidentified gunmen to sign an unofficial paper that said he was barred from entering Russian soil for five years.
Crimean Tatars make up roughly 13 percent of Crimea's 2.1 million people. They were deported en masse to Central Asia by Moscow in 1944 before being allowed to return to their homeland in the late 1980s as the Soviet Union began to collapse.