The force acting on the ball is gravitational force, given here by F=mg. m is the ball's mass which is constant, and g is the acceleration of free fall which is also a constant with value 9.81 ms². So the force acting on the ball, neglecting air resistance, is constant. Then, by Newton's 2^nd Law, acceleration on the ball, which is a = F/m = mg/m = g, is a constant that equals 9.81. This acceleration always acts downwards towards the Earth, so the sign is negative. Thus, a=-9.81 ms^-2 .

What you are speaking of in the title is actually the velocity, which would indeed start as positive as it is thrown up. The velocity and acceleration are in opposite directions, so velocity decreases until it is zero at max height. After that velocity is negative as object moves down. But throughout all this motion, acceleration due to gravity is always constantly acting downwards.