Integrated microfluidic circuits' applications range from microbiology to quantum physics. Here we propose a programmable microcontroller-mediated platform, able to control and automate Large-Scale Integrated (LSI) microfluidic circuits. Our platform supports local and remote control of flow and data acquisition. Demonstration includes regulation schemes of real-time flow modulation. We utilized Raspberry-Pi as a controller and developed a Java-based stand-alone software to control solenoid valves and pressure sources, as well as to parse text-based instruction sets. We used node.js to define an embedded web server to allow network capabilities and developed an Android application for mobile-based control. Messaging protocol includes broadcasting and verifications to allow synchronization among the control sources. The system can be rapidly extended to support additional pressure sources, control and flow lines, and microfluidic components. Our system offers a comprehensive solution for establishing automation protocols and perfusion sequences in integrated microfluidic circuits.