Migraine is common in children, but few specific drugs are available. We performed an open-label comparison of effects of two nutraceutical preparations (ginkgolide B vs. Griffonia simplicifolia extract) on outcomes in 374 school-age children (mean 10.7 years) with migraine without aura. Half of them received ginkgolide B; and half, Griffonia simplicifolia. Both preparations were given orally twice a day for 6 months. Patients kept a headache diary. Outcomes at the beginning and end of treatment were compared. Both preparations reduced all outcome measures after 6 months of treatment. However, reductions in headache frequency, duration and intensity, PedMIDAS score and behavioural reactions to headache were significantly greater in the ginkgolide B group. Both nutraceutical treatments appear promising in paediatric migraine without aura, particularly because of their lack of side effects. However, the ginkgolide B preparation was significantly more effective in the medium-term (6 months).