Lithuania's swimming federation said earlier this month that Meilutyte faced a suspension of up to two years for missing three drug tests, meaning she would be ruled out of the 2020 Tokyo Olympics.
"The swimmer took full responsibility for missing all tests," the federation said, adding that Meilutyte had failed to properly inform international anti-doping authorities about her whereabouts.
Lithuania's anti-doping chief Kristina Jagminiene described it as an "unfortunate mistake".
Meilutyte, who has never failed a doping test, was a star of the 2012 London Games, where as a 15-year-old she won the 100 metres breaststroke event.
She also won the gold at the world championships in Barcelona a year later.
"I am ready to start a new chapter of my life. Thank you all who supported me on this road", she said in a statement.
Meilutyte said she wanted to return to her studies and "experience simple things, to grow, to better understand myself and the world".
Last year, Meilutyte admitted she was suffering from depression.
During her swimming career, she won 20 gold medals in top international competitions, according to Lithuania's swimming federation.
Her last event was the World Championships in China last December where she failed to qualify for the finals.
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