In a closed meeting of the federation’s executive committee on Wednesday, Eimontas received 73 votes out of 78.
“I am touched and would like to thank delegates for their trust. I believe that during my four-year term, we will be able to raise football to a qualitatively new level,” Eimontas said after the secret ballot which was held in Kaunas, Lithuania’s second biggest city.
Eimontas, 39, was previously the federation’s general manager and deputy of its controversial outgoing president Julius Kvedaras.
The federation and Kvedaras are under investigation by state anti-fraud investigators.
Officers from the Financial Crime Investigation Service carried out searches of the headquarters of Lithuanian Football Federation and of the home of Kvedaras’ home before Christmas.