Polyanions of the aromatic origin such as dianion of benzene (C6H6 2−) are generally metastable having negative electron affinity (EA). However, the de-protonated species of these anions such as doubly-deprotonated dianions of benzene (C6H4 2−) can have higher proton affinity compared to the magnitude of the negative EA, which can trigger an intra-molecular proton transfer besides the electron auto-detachment. Such species though may exhibit resonances as in the temporary anions and cannot be treated using the conventional variational methods of the quantum mechanics. In this work, we discuss the metastability, through a nuclear-charge stabilization method, for the poly-deprotonated dianions and trianions of benzene, while exploring the intra-molecular proton-transfer reaction pathways using the conventional quantum mechanical methods, for the isomerization between the isomeric doubly-deprotonated benzene dianions, namely the ortho-, meta-, and para-C6H4 2−, as well as between the isomeric triply-deprotonated benzene trianions, namely the 1,2,3-, 1,2,4-, and 1,3,5-C6H3 3− in their singlet state. For this, the potential energy surfaces of the polyanionic species, in particular those of the doubly-deprotonated dianions, are successfully explored through an automated and systematic search performed using the global reaction route mapping method. The computations performed at the levels of the MP2, DFT with and without dispersion, and CCSD(T) theories, identified elusive reaction pathways for the isomerization between the anionic species of the poly-deprotonated benzene. Notably, a single-step isomerization between the ortho- and para-C6H4 2− dianions is observed to proceed via a direct 1, 3-proton shift in an unconventional transition state involving a puckered benzene ring in a nearly half-boat conformation. However, for the isomerization between C6H3 3− benzene trianions, the present work was able to reveal pathway only between 1,2,4-C6H3 3− and 1,3,5-C6H3 3− trianions, indicating the problems like variational collapse inherent with the conventional methods while dealing with the molecular polyanions. However, the lifetime of the metastable molecular ions investigated in this work is estimated to be of the order of only a few femtoseconds, an order of magnitude higher than the proton-transfer rate along the proposed isomerization pathways, but this study is able to provide valuable insights into the mechanism of proton transfer in the presence of a competing electron auto-detachment process.