Regarding the Fraction class, a couple of things: first fractions have numerators and (nonzero) denominators so I would get rid of the no argument constructor. (I would also point out - although it's not a big deal at this stage - that people are wary of calling nonprivate methods like your setXXX() from within the constructor. Things can go wrong if the Fraction class is ever subclassed by something that replaces the setter methods by other ones.)

A bigger problem is that your equals() insists on have both the numerators and denominators equal. But real fractions don't work that way. Suppose you have two fractions n1/d1 and n2/d2 then they are equal whenever n1*d2==n2*d1. For example 2/6 equals 1/3 because 2*3==1*6.

As for the driver...

for(int i = 0; i < size; i++){
Fraction a = new Fraction(numerator[i],denominator[i]);
}

This code does nothing with

*a*, which I guess is where you're stuck. But you haven't told us what the driver is actually supposed to do. (Check for two equal fractions entered one after another? Check for *any* equal fractions? Something else?) So it's hard to know what to suggest.

(I prefer the idea you've commented out, of having an ArrayList<Fraction> in place of those parallel arrays of ints. Whatever you're supposed to do will, most likely, be more naturally done with a list: read a line, construct a fraction, and put the fraction into the list until you've finished the file. Then do whatever with the list of fractions. If the question asks you to do something like remove duplicate fractions then a Set is better than a List.)