"Oliver Glasner has shown in the last two years at Wolfsburg that he is able to work at the absolute top level and develop young players," said Frankfurt director Axel Hellmann in a statement.
Glasner, 46, led Wolfsburg to a top-four finish last season, but will now forego the chance to lead the club in the Champions League in order to join Eintracht, who finished fifth.
His move to Frankfurt, who will play in the Europa League next season, continues a trend of Bundesliga managers moving to clubs lower down the table.
He will take over from fellow Austrian Adi Huetter, who is leaving Frankfurt for Borussia Moenchengladbach, a club who missed out on European football entirely by finishing eighth.
Glasner, who had remained tight-lipped over his future in recent weeks, said the decision to leave Wolfsburg had "not been easy".
"Eintracht Frankfurt is an exciting club. The emotions in the city and the region are great," he added.
The Austrian will be charged with guiding Frankfurt through a period of upheaval, with many key figures in the club leadership set to leave this year.
As well as Huetter, the club is set to lose sporting directors Fredi Bobic and Bruno Huebner, who are widely seen as the architects behind Frankfurt's success in recent years.
The club won the German Cup in 2018, reached the Europa League semi-finals the following year and only just missed out on a top-four spot this season.