The language represented by an NFA is regular. The complement of a regular language is regular. Every regular language can be represented by an NFA. Hence NFAs can be "complemented".
More concretely, convert your NFA to a DFA and then complement it.
What you're really asking is, probably, is there a more direct way to complement NFAs. There are examples in which there is a large gap between the NFA complexity of a language and its complement. For example, the language of all words over $\{1,\ldots,n\}$ which don't contain all symbols is accepted by an NFA of size $n$ (or $n+1$ if you don't allow multiple starting states), but its complement needs exponentially many states $2^n$.