In this paper we present a parallel wavelet transform based implementation of Finite element method for solution of multiscale PDEs. The parallel wavelet transform is adopted from and is used for parallelizing a wavelet based finite element code. The parallel wavelet transform results in optimal load balancing with minimum communication requirements. The algorithm is highly scalable approaching perfect speedup as the problem size is increased. The implementation details of the parallel wavelet transform and its application in solution of some linear elliptic PDEs are discussed.