The transport and Golgi organization 2 (TANGO2) gene has been identified to cause a rare recessive genetic disorder known as TANGO2-deficiency disorder (TDD). TDD is a multisystemic disorder that can affect different organs including the brain, heart, and muscles, presenting as recurrent metabolic crises, muscle weakness, and neurological symptoms including developmental delay and seizures. In a TANGO2-KO Cal51 cell line model, N-glycomics of the TANGO2-KO cell line showed a significant change in glycomics profile, that was also corroborated with RNAseq transcriptomics showing increased mRNA levels of the respective glycosyltransferases. To investigate the effects of TANGO2-KO on the glycans in the brain of a mouse model, we profiled the polysialic acid (polySia), glycosaminoglycans (GAG), glycolipid glycans (GSL), and protein N- and O-glycans (NG, OG) of the cortex of the TANGO2-KO mice using the Same Sample Sequential Multi-Glycomics workflow. Overall, we observed a severe decrease in chondroitin sulfate GAG disaccharides, and a mild decrease in sialylation across GSL, NG and OG, resulting in a broad decrease in negatively charged glycoconjugates. When comparing against an independent DDA LFQ proteomics acquisition of the same mice model, amongst the glyco-enzymes, only sialic acid synthase (NANS) and chondroitin polymerising factor (CHPF) was also found to be significantly down regulated in the brain, correlating with the changes observed by the multi-glycomics analysis. This overall decrease in negatively charged glycoconjugates due to the loss of TANGO2 function might thus relate to the neurological impairments of TDD.