Graphene doped with heteroatoms is known to create a unique electronic structure with comparatively much higher active sites by the synergistic coupling effect. However, in the earlier attempts, the atomic structure of such co-doped graphene could not be altered; thus, there is a lack of reports discussing the influence of the atomic arrangement in the catalytic performance of the co-doped graphene. Here, by co-doping P and N atoms in graphene as a model system, we present a facile and two-step process wherein the sequence of doping helps in manipulating the heteroatom substitution, which is of great importance in defining better crystallinity and conductivity and favorable elemental functionalities and hence improving catalytic performance. The present method provides a clean, flexible, binder-free, and readily available electrocatalyst that avoids tedious conventional synthesis and device fabrication steps. The highest P-doping percentage (6 at. %) in the present work is superior to previous reports (3 at. %). By altering the sequence of N- and P-doping, the co-doped graphene electrode displayed excellent performance, with an increment of 148% in the sp2 domain size and enormous lowering in overpotential and Tafel slope (78%). Further, the efficiency of the hydrogen evolution reaction catalyst sustains >98% for 20 h, which is significantly higher than the well-known MoSx (63%). Although here the P-N co-doped system was utilized as a proof of concept, this method could be adapted for other versatile co-doped graphene. This work may pave the way for the development of co-doped graphene-based devices where manipulation of atomic arrangement can result in a structure with properties desirable for catalytic or electronics applications.