The businessman put his name forward to the country's electoral commission to stand in the May poll.
But the constitution requires candidates to be of Lithuanian origin – Romanov was born in Russia and only moved to the Baltic State aged nine.
His application was turned down by the country's electoral authorities, who rejected it unanimously.
"The commission voted unanimously that he does not qualify to be of Lithuanian origin and by law he cannot stand as president," deputy chairman of the electoral commission Saulius Katuoka said.
The former Soviet submariner, who took over at Tynecastle in 2005, is a popular figure in Lithuania.
In 2007, he came top in TV show Dancing with the Stars, a Lithuanian version of Strictly Come Dancing.
But Romanov has courted controversy during his reign at Hearts, sacking a succession of managers and popular players.
He also controls the Lithuanian club FBK Kaunas and the Belarusian Premier League side FC MTZ-RIPO.
He is chairman of UBIG Investments, which is the majority shareholder in Hearts.
Romanov's main business interest is a substantial stake in the Lithuanian bank Ukio bankas.