The best thing to do is to ask the teacher for the maximum size of input, both the maximum number of words and the maximum size of a word. If you can't do that, then you have to make the array very large:
Code:
#define MAX_WORDS 1000000
#define MAX_WORD_SIZE 50
// In main (perhaps):
static char words[MAX_WORDS][MAX_WORD_SIZE]; // 50MB
If the array is defined inside a function (usually the best option) then you should make it "static" so that it is not stored on the stack. Although be aware that that means the storage will never be deallocated, which is probably okay in your case.
You also need to ensure that you don't go beyond these bounds, unlikely as that may be (with normal, error free, non-malicious input).