Work Energy Theorem and Potential Energy violation?

I came across a rather confusing topic about Work Energy Theorem and Potential Energy applied in lifting a particle.I will be glad if anyone clears it for me.

Consider a particle at a height =0.Potential Energy is considered as zero at height=0.Now it is lifted to a position where height is h so that Potential Energy of the particle is increased by a value mgh where m is the mass of it,g is the gravitational acceleration.Or in other words energy possessed by the particle is increased from zero to mgh.Now the problem begins.
Net work done on the system W(net)=Change in Kinetic energy.But here initial and final kinetic energy of the particle is considered to be zero since the particle is stationary at initial and final positions.This means there is no change in energy of the particle.Because energy is something required to do work.But since net work is zero ,then energy of the particle should be constant.And I just can't apply energy function for this case
Potential energy U(final)-U(initial)=-W=K(initial)-K(final)
But W=0.Then how can I say potential energy change is zero since it is obvious that it possesses mgh energy?