A message passing interface (MPI) based parallel simulation algorithm is developed to simulate protein behavior in non-linear isoelectric focusing (IEF). The mathematical model of IEF is formulated based on mass conservation, charge conservation, ionic dissociation-association relations of amphoteric molecules and the electroneutrality condition. First, the concept of parallelism is described for isoelectric focusing, and the isoelectric focusing model is implemented for 96 components: 94 ampholytes and 2 proteins. The parallelisms were implemented for two equations (mass conservation equation and electroneutrality equation). The CPU times are presented according to the increase of the number of processors (1, 2, 4 and 8 nodes). The maximum reduction of CPU time was achieved when four CPUs were employed, regardless of the input components in isoelectric focusing. The speed enhancement was defined for comparison of parallel efficiency. Computational speed was enhanced by maximum of 2.46 times when four CPUs were used with 96 components in isoelectric focusing.