A seemingly inconspicuous item at first, April purchases the flute at the Marcurian docks in order to distract the Mo'Jaal so that Captain Nebevay will sign the delivery list. She buys it outside the city gates, from the Music Vendor who only communicates through playing his instruments. The flute costs one Aren and is the only instrument April can afford; luckily she knows how to play one.
Later in the game, the flute becomes very important to April as a means of calling Crow to her aid, both in Arcadia and later, magically, in the Guardian's Realm. It may be that, in the same way as April's painting helps her to Shift, playing the flute allows her to unconsciously use her own magic.
Obtained from the Marcuria docks.