Caribou is a flexible data acquisition system for prototyping silicon pixel detectors. The core of the system consists of the Control and Readout (CaR) board, a versatile module providing the hardware environment for various target ASICs, including powering and slow-control infrastructure, and high-speed full-duplex GTX links up to 12.5 Gbps. The CaR board connects to a Zynq system-on-chip board which runs a fully-featured Yocto-based Linux distribution (Poky) and a data acquisition software (Peary). Using the Caribou system significantly reduces the time required to test and debug detector prototypes by providing ready-to-use peripheries and their software interfaces together with a widely adjustable data acquisition framework that is suitable for a variety of detectors. The paper describes the hardware and software architecture of the system, its capabilities, and examples of projects where it has been used.