A continuous flow ozonolysis method combined with a multi-step flow sequence is developed for the synthesis of the drug ivacaftor for the first time. Safe ozonolysis, a continuous flow quadruple reaction to construct a quinolone scaffold, and inline extraction followed by continuous phase separation are the key features of the present work. The feasibility of using a continuous mixed flow reactor, commonly referred to as a continuous stirred tank reactor (CSTR), is also investigated for the relatively slow reaction step. The current integrated multi-step flow synthesis can produce 7.2 g of the drug ivacaftor per day on a laboratory scale, which is sufficient to treat 50 patients per day. The present route can also be used as a general route for the synthesis of other related drugs such as quinolone antibiotics.