In this paper, we give an algorithm which, given a set F of at most n-k faulty nodes, and two sets S={s1, , sk} and T = {t1,, tk}, 1kn, of non-faulty nodes in n-dimensional hypercubes Hn, finds k fault-tree node disjoint paths sitje, where (j1, , Jk) is a permutation of (1, , k), of length at most n + k in O(kn log k) time. The result of this paper implies that n disjoint paths of length at most 2n for set-to-set node disjoint path problem in Hn can be found in O(n2 log n) time.