Involved in the degradation of prenylcysteine. Cleaves specifically the thioether bond of S-farnesyl-L-cysteine and has no activity with S-geranylgeranyl-L-cysteine. Recognizes also N-acetyl-farnesylcysteine and may have a role in deprenylation of farnesylated proteins. H2O + O2 + S-(2E,6E)-farnesyl-L-cysteine = (2E,6E)-farnesal + H2O2 + L-cysteine Expressed in seedilings, flowers, stems, leaves and roots. Plants with decreased levels of farnesylcysteine lyase exhibit delayed germination and hypersensitivity to abscisic acid. Belongs to the prenylcysteine oxidase family.