The proton transfer between two nitrogen atoms (N1 and N3) in a molecule of phenyl urea is an important process in the synthesis of 1-phenylimidazolidine-2,4-dione. Three pathways of the proton transfer have been investigated using Density Functional Theory (DFT). With negative N1 phenyl urea, the transformed double bond of N1-C2 connects N1, C2, and N3 into a benzene conjugate system, making the structure more stable than negative N3 phenyl urea. Intermolecular proton transfer was found to be the primary manner of protein transfer at 300 K. Both negative N1 and negative N3 exist and the former is primal. The proton transfer is very fast, and the diluted solution may slow down the rate but produce much more negative N1 as well.