The British star won the award for both Best Actress in a Comedy Series, beating The Marvellous Mrs Maisel star Rachel Brosnahan.
Elsewhere, Bill Hader took home Best Actor in a Comedy Series for Barry, while Marvellous Mrs Maisel stars Alex Borstein and Tony Shalhoub won in the supporting categories.
Earlier in the evening, Waller-Bridge had won Outstanding Writing in a Comedy Series for Fleabag.
Phoebe Waller-Bridge had a big night at this year’s Emmys.