Yes (but also no). The initial form of this equation is

    (mc^2)^2 = E^2 - (pc^2)^2

The Pythagorean theorem tells you the length of a 2D vector when you know x and y lengths. Here mc^2 is the length of the 4-momentum vector [E, pc^2] (where p is a standard 3D vector). However since our 4D spacetime is not Euclidian but Minkowskian the sign in the generalised Pythagoras theorem is a minus and not a plus.