Acceleration is defined as the change in velocity per unit time. Suppose you throw it upward with a positive velocity of 19.6 m/s. After one second it will have slowed to 9.8 m/s, so it's acceleration is:
Now consider its motion from t = 2 seconds to t = 3 seconds. At t=2 it reaches its max altitude and has v=0. From t=2 to t=3 it starts to fall, and reaches a velocity of -9.8m/s at t=3. Its acceleration is therefore:
Again. It's negative. Under gravity the acceleration of an object in free fall (meaning only gravity is acting on it) is always -9.8 m/s^2, regardless of its velocity or direction of movement.