The cytosolic peptide:N-glycanase (PNGase, NGLY1 in mammals) is an enzyme that removes N-glycans from misfolded glycoproteins. NGLY1 contributes to cytosolic glycan degradation (non-lysosomal glycan degradation) and is one of the quality control systems for newly synthesized proteins, i.e., ER-associated degradation (ERAD). NGLY1 is also responsible for the activation of a transcription factor, NFE2L1, which participates in several stress responses, including regulation of proteasome subunit expression and oxidative stress. In 2012, NGLY1 deficiency, a human genetic disorder caused by the biallelic mutations in the NGLY1 gene, was discovered. Since then, research on the physiological functions of NGLY1 and the pathogenic mechanism of NGLY1 deficiency has expanded rapidly. Here, we will briefly overview the early history of NGLY1 research and then introduce its versatile functions. We will also provide mechanistic insights into the pathogenesis of NGLY1 deficiency based on studies using model animals, such as worms, flies, and rodents.