Recent advances in digital microfluidics have enabled lab-on-a-chip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Basic operations such as droplet dispensing, mixing, dilution, localized heating, and incubation can be carried out using a 2-D array of electrodes and nanoliter volumes of liquid. The number of independent input pins used to control the electrodes in such microfluidic “biochips” is an important cost-driver, especially for disposable printed circuit board devices that are being developed for clinical and point-of-care diagnostics. However, most prior work on biochip design-automation has assumed independent control of the electrodes using a large number of input pins. We present a broadcast-addressing-based design technique for pin-constrained multifunctional biochips. The proposed method provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with “compatible” actuation sequences. We also describe two scheduling methods to map fluidic operations on the pin-constrained design, in order to minimize the completion time while avoiding pin-actuation conflicts. The proposed methods are evaluated using multifunctional chips designed to execute a set of multiplexed bioassays, the polymerase chain reaction, and a protein dilution assay.