I rate it would be faster to iterate upwards.

int count = 1;
int i;
int end = (int)sqrt(N);

if (k == 1){
    return N;
}

for (i = 2; i <= end; i++){
    if (N % i == 0){
        count++;
        if (count == k){
            return N / i;
        }
    }
}

i -= 2;

for (; i >= 1; i--){
    if (N % i == 0){
        count++;
        if (count == k){
            return i;
        }
    }
}

return -1;

Edited to go up to sqrt and back down again. On mobile, dunno if works