This paper discusses the implementation of proportional resonant (PR) current controllers for a Voltage Source Converter (VSC) with LCL filter which is synchronized to the grid by virtual flux (VF) estimation with inherent sequence separation. Even though there is an extensive amount of literature and studies on the PR current controller for tracking the current reference of a VSC in the stationary reference frame, there is no discussion taking into account voltage sensor-less operation based on virtual flux estimation with an LCL-filter. Separate estimation of the positive and negative sequence virtual flux components at the grid-side of the LCL-filter, as well as current sequence separation, using the Second Order Generalized Integrator-Frequency Locked Loop (SOGI-FLL) is presented as part of a proposed method. The LCL filter is characterized in order to reduce the parameter deviation that might affect the virtual flux estimation. The stability of the proposed method is analyzed in the frequency domain while the operation and performance of the proposed system is verified by simulation studies.