Evangelion Store Tokyo-01
Time Out says
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The official shop for anime franchise Evangelion should be able to satisfy all your mecha needs, with everything from clothing to cakes, plus a few limited edition items that are guaranteed to make your otaku pals jealous.
UPDATE: The Evangelion Store is moving from Harajuku to Ikebukuro, and will be opening in the renovated P'Parco building on October 3, 2014.
P'Parco 2F 1-50-35 Higashi-Ikebukuro, Toshima-ku