Can a body be in equilibrium when only one force acts on the body? I think that when we throw a body in air, at top point the body is in equilibrium but gravitational force is still acting. Is this correct?
 A: You are confusing equilibrium with $0$ velocity.
Equilibrium occurs for when the net force is $0$ $$\Sigma \vec F_i=0$$
If you only have one force $\vec F$ then it must be that this force is $0$ 
$$\Sigma \vec F_i=\vec F=0$$
In other words, if we want to be in equilibrium with only one force, it must be that the force is $0$ (there is no force! A contradiction to the assumption that we have one force acting on the body). So, we see that we cannot be in equilibrium with only one force acting on the object.
As for your example of an object at the top of its trajectory, you are correct in saying here the velocity is $0$. But this is not equilibrium. The gravitational force here is constant, and a single force, so we do not have equilibrium.

Addition based on comments
Technically for equilibrium to occur you must also have the net torque about any point equal to $0$ $$\Sigma \vec \tau _i=0$$
This condition is not important for your problem (usually we treat projectiles as point objects in intro physics), so I did not focus on this aspect. As long as one condition of equilibrium is not met (net force is not $0$), then we do not have equilibrium. Therefore, it was sufficient to just talk about the case of one force without considering the net torque due to that single force.
A: First of all: According to General Relativity there is no gravitational force. So when the body is thrown up into the air there is only a force applied during the throw, before the body leaves that hand. After that the body follows its trajectory through space bent by mass. In this example the mass is probably planet earth.
In classical mechanics though, the gravitational force is always working. There is no equlibrium at any time. The body is accelerated by the throw and after being thrown the gravitational force is working on the body, first slowing it down more and more, up to a halt, and then acceleration it into the opposite direction.
To adress the point where the possible misconception is coming from:
The point in time when the velocity is 0 is infinitessimal small and even at that point the gravitational force is working. Otherwise the acceleration into the other direction would never take place.
