The Bordetella bipA gene is expressed maximally when the BvgAS phosphorelay is semi-active, i.e. in the Bvg-intermediate (Bvgi) phase. We used a BvgA-FeBABE cleavage approach together with site-directed mutagenesis and bipA–lacZ fusion analyses to determine precisely where BvgA-phosphate (BvgA∼P) binds at the bipA promoter and how that binding contributes to the complex transcription pattern displayed by bipA. BvgA∼P bound with high affinity and cooperatively with RNAP to sequences at the bipA promoter immediately 5′ to and overlapping those bound by RNAP to activate transcription under Bvgi phase conditions. bipA therefore, like fhaB, appears to be similar to classical class-II promoters with regard to the mechanism by which its transcription is activated. BvgA∼P bound with relatively low affinity to sequences immediately 3′ of those bound by RNAP at the bipA promoter and this binding mediated repression of bipA transcription under Bvg+ phase conditions. BvgA∼P binding to these sequences occurred simultaneously, if not cooperatively, with RNAP, indicating that BvgA∼P represses bipA expression by inhibiting transcription initiation and/or elongation, rather than by competing with RNAP for binding. As bipA is the first Bvgi phase gene to be characterized, and the first gene shown to be repressed by BvgA∼P directly, our results will provide a basis for comparison as additional Bvg-regulated genes are identified and characterized.