We present a hypertensive child with a co-existence of polyarteritis nodosa, anti-phospholipid antibodies (aPL), methylenetetrahydrofolate reductase (MTHFR) mutation and increased lipoprotein a level. Elevated renin, aldosterone and aPL levels, micro-aneurysms, occlusion and thrombosis at left and right renal artery were found. Anti-hypertensive agents, prednisolone and pulse cyclophosphamide therapy were started and a stent was inserted in the left renal artery. Two months later, brain magnetic resonance imaging/magnetic resonance imaging angiography showed acute infarct area of the left parietofrontal lobe and middle cerebral artery stenosis. We found bilateral peripheral neuropathy, persistent aPL and elevated Lp(a) level and heterozygous A1298C/MTHFR mutation. Intravenous immunoglobulin and low-molecular-weight heparin treatment was added. In conclusion, our observation suggests that in patients with systemic vasculitis, such as polyarteritis nodosa, aPL are probably associated with greater thrombotic risks. The investigation of the LP(a) levels and MTHFR mutations as a synergic pro-coagulant effect might also be considered for determining patients with vasculitis at risk for severe thrombotic events.