The Cherenkov Telescope Array (CTA) Observatory must be capable of issuing fast alerts on variable and transient sources to maximize the scientific return. This will be accomplished by means of a Real-Time Analysis (RTA) pipeline, a key system of the CTA observatory. The latency and sensitivity requirements of the alarm system impose a challenge because of the large foreseen data flow rate, between 0.5 and 8 GB/s. As a consequence, substantial efforts toward the optimization of this high-throughput computing service are envisaged, with the additional constraint that the RTA should be performed on-site (as part of the auxiliary infrastructure of the telescopes). In this work, the functional design of the RTA pipeline is presented.