Involved in the initial and rate-limiting step of peroxisomal beta-oxidation of straight-chain saturated and unsaturated very-long- chain fatty acids (VLCFAs) (PubMed:15060085, PubMed:17458872, PubMed:17603022, PubMed:32169171, PubMed:33234382, PubMed:7876265). Catalyzes the desaturation of fatty acyl-CoAs that have a saturated bond between C2 and C3 (2,3-saturated acyl-CoA) to 2-trans-enoyl-CoAs ((2E)-enoyl-CoAs), and donates electrons directly to molecular oxygen (O(2)), thereby producing hydrogen peroxide (H(2)O(2)) (PubMed:17458872, PubMed:17603022, PubMed:7876265). May play a role in peroxisomal beta-oxidation step in polyunsaturated fatty acids (PUFAs) biosynthesis. Possibly regulates systemic levels of docosahexaenoic acid (DHA, C22:6n-3) through a process involving endoplasmic reticulum desaturation and elongation of alpha-linolenic acid (ALA, C18:3n-3) to form tetracosahexaenoic acid (THA, C24:6n-3), which is then beta- oxidized to DHA in peroxisomes (Probable). Involved in VLCFA-dependent hepatic-to-adipose tissue inter-organ signaling in response to diet. Through hepatic beta-oxidation of THA, may regulate THA systemic levels and THA-dependent activation of FFAR4 signaling in adipocytes, limiting adipose tissue thermogenesis (By similarity). {ECO:0000250|UniProtKB:Q9R0H0, ECO:0000269|PubMed:15060085, ECO:0000269|PubMed:17458872, ECO:0000269|PubMed:17603022, ECO:0000269|PubMed:32169171, ECO:0000269|PubMed:33234382, ECO:0000269|PubMed:7876265, ECO:0000303|PubMed:10903473, ECO:0000303|PubMed:35951481, ECO:0000303|PubMed:7685190, ECO:0000305|PubMed:11734571, ECO:0000305|PubMed:20195242}. [Isoform 1]: Shows highest activity against medium-chain fatty acyl-CoAs. Shows optimum activity with a chain length of 10 carbons (decanoyl-CoA) in vitro. {ECO:0000269|PubMed:17458872, ECO:0000269|PubMed:17603022}. [Isoform 2]: Is active against a much broader range of substrates and shows activity towards long-chain and very-long-chain fatty acyl-CoAs. {ECO:0000269|PubMed:17458872, ECO:0000269|PubMed:17603022}. This is the function of ACOX1 (acyl-CoA oxidase 1, ENSG00000161533).