Yes. In the circular motion of a body, the velocity is tangential to the circle but the force and acceleration will be along the radius towards the centre. Since the radius and tangent are normal to each other, velocity and acceleration are perpendicular.
Also, when an object is thrown by making an angle with horizontal [Projectile Motion], at the highest point, the velocity is directed horizontally. But due to gravitational force, the object has acceleration due to gravity in vertically downward direction. So, at that instant, velocity and acceleration are in perpendicular directions.
[Read: Motion in a Straight Line]