Sialylation plays an important role in self‐recognition, as well as keeping the complement and innate immune systems in check. It is unclear whether the reduced sialylation seen during aging and in mice heterozygous for the null mutant of UDP‐N‐acetylglucosamine 2‐epimerase/N‐acetylmannosamine kinase (Gne+/−), an essential enzyme for sialic acid biosynthesis, contributes to retinal inflammation and degeneration. We found a reduction of polysialic acid and trisialic acid expression in several retinal layers in Gne+/− mice at 9 months of age compared to Gne+/+ wildtype (WT) mice, which was associated with a higher microglial expression of the lysosomal marker CD68. Furthermore, the total number of rod bipolar cells was reduced in 12 months old Gne+/− mice in comparison to WT mice, demonstrating loss of these retinal interneurons. Transcriptome analysis showed up‐regulation of complement, inflammation, and apoptosis‐related pathways in the retinas of Gne+/− mice. Particularly, increased gene transcript levels of the complement factors C3 and C4 and the pro‐inflammatory cytokine Il‐1β were observed by semi‐quantitative real‐time polymerase chain reaction (sqRT‐PCR) in 9 months old Gne+/− mice compared to WT mice. The increased expression of CD68, loss of rod bipolar cells, and increased gene transcription of complement factor C4, were all prevented after crossing Gne+/− mice with complement factor C3‐deficient animals. In conclusion, our data show that retinal hyposialylation in 9 and 12 months old Gne+/− mice was associated with complement‐related inflammation and lysosomal microglia response, as well as rod bipolar cells loss, which was absent after genetic deletion of complement factor C3.