The 24-year-old striker has scored three goals in nine games for the Latics since joining on loan in January.
Football League rules allow 'long loan' moves to be converted into a full-time move outside of the transfer window, and with Waghorn's Foxes contract due to expire at the end of the season, Wigan boss Uwe Rosler was keen to tie the former England Under-21 international down before any of their Championship rivals swooped.
"Martyn has impressed us all since he arrived in January," he told the club's official website. "On the pitch, he has added something different, scoring and assisting crucial goals and he gives us another tremendous option from set pieces.
"Off the pitch he has a real professional attitude, he works hard and has fitted in perfectly to the dressing room.
"I am delighted we have been able to get a young English player with a proven track record on a free and I am sure he will keep helping us this season and become a real crowd favourite here at the DW."
Waghorn netted 20 times in 119 games for Leicester over a season-long loan spell at the King Power Stadium and three more years during which he was sent out to Hull City, Millwall and lastly Wigan.