"Today, the decision was made with the community chair, Faina Kukliansky, to resume the activity of the community and synagogue," the JCL said in a statement.
The premises were closed on Tuesday in response to received threats following rising tensions over the Vilnius authorities' decision to remove memorial signs to Kazys Skirpa and Jonas Noreika, two controversial figures in Lithuania.
The JCL says the decision follows President Gitanas Nauseda and Prime Minister Saulius Skvernelis' reaction to the closure, saying that representative of all nations can feel safe in Lithuania.
Kukliansky said earlier she had not turned to the police over the threats they were not real threats but letters of threatening nature.
Meanwhile, several Jewish organizations disagreeing with Kukliansky called her decision to close the synagogue and other premises wrong.
Tensions have risen in Lithuania in recent weeks following Vilnius officials' decisions to rename a street named after Kazys Skirpa, a controversial 20th century Lithuanian diplomat and military officer, and to remove a memorial plaque to Jonas Noreika, a high-ranking military officer accused of collaborating with the Nazis, due to their activities during WWII.
A rally was held by over 300 people in central Vilnius on Wednesday, with participants stressing Noreika and Skirpa's contribution to the anti-Soviet movement. Meanwhile, the Jewish community has welcomed the decisions.