Board Thread:Character Discussion/@comment-26106001-20150213163045/@comment-25355646-20150213165411

I think inorder for the sacrifice with Henry's heart to work, he needed Henry to believe in him at least once (like he told Wendy in 3x07. Pan said he needed to control Henry's belief in him).

Another explanation is that Pan did have some humanity left in him and he didn't feel comfortable with just taking Henry's heart at first.