Nanopores – nanometer-size channels hold significant promise for numerous applications: DNA sequencing, sensing, biosensing and molecular detectors, and catalysis and water desalination. However, these applications require accurate control over the size of the nanopores. Since graphene is often mentioned as a promising material to host nanopores, we have performed realistic computer simulation studies of regrowth and healing of graphene nanopores of different sizes ranging from 30 to 5 Å. Our simulations clearly point to at least two distinct healing mechanisms for graphene sheets: edge attachment (where carbons are attached to the edges of the graphene sheet/pore) and direct insertion (where individual atoms insert directly into a sheet of graphene, even in the absence of the edges). The insertion mechanism is a surprising prediction that points to the growth process that would be operational in pristine graphene. We have uncovered an unusual dependence in the speed of nanopore regrowth and the structure of “healed” areas as a function of its size in a wide range of temperatures. Our findings point to significantly more complicated pathways for graphene annealing. They also provide an important enabling step in the development of graphene-based devices for numerous applications in nanotechnology. Our results suggest the possibility to control the final size of healed nanopore by terminating the annealing at a prescribed time dependent on the temperature.