Matrix metalloproteinases (MMPs) and tumor necrosis factor (TNF)-α contribute to the pathogenesis of several ocular diseases. In this study, we aimed to determine the role of interaction between TNF-α and MMP-9 in capillary degeneration. In rats, retinal injury was induced by intravitreal injection of N-methyl-D-aspartic acid (NMDA) at postnatal day 7. We examined 1) the effects of blocking MMP-9 and TNF-α signaling pathway on capillary degeneration, 2) changes in protein levels and distribution of MMP-9 and TNF-α, and 3) the interaction between MMP-9 and TNF-α in regulating the expression level of each protein in retinas of NMDA-injected eyes. Intravitreal injection of GM6001, an MMP inhibitor, or TNF-α neutralizing antibody (anti-TNF-α Ab) attenuated capillary degeneration in retinas of NMDA-injected eyes. Protein levels of TNF-α increased 2 h after NMDA injection, whereas those of MMP-9 increased 4 h after the injection. Anti-TNF-α Ab suppressed activation of MMP-9 in retinas of NMDA-injected eyes, whereas GM6001 diminished the TNF-α protein expression. Incubation of recombinant TNF-α with supernatants of homogenized retina increased protein levels and activity of MMP-9. These results suggest that TNF-α and MMP-9 collaboratively contributes to the progressive capillary degeneration in injured retinas.