This work presents the construction and application of boron-doped diamond (BDD) thin film electrode as sensor for the determination of three β-agonists, viz. salbutamol, terbutaline and clenbuterol. Although well-known as a chemically inert material, BDD film however shows fouling in detection of these compounds using fixed- potential mode amperometry. A suitable waveform for pulsed amperometric detection (PAD) was developed and used to determine the agonist compounds. It was seen that the developed PAD significantly refreshed the BDD surface for long-term detection in flow injection analysis. Linear working ranges were 0.5-100 µM, 1.0-100 µM and 0.5-50 µM for salbutamol, terbutaline and clenbuterol, respectively. The developed PAD-BDD system was applied to successfully determine salbutamol and terbutaline in commercial pharmaceutical products. The methods were validated with a capillary electrophoresis method.