REMUS-II (REconfigurable MUltimedia System 2) is a coarse-grained dynamically reconfigurable computing system for multimedia and communication baseband processing. This paper proposes a real-time H.264 baseline profile encoder on REMUS-II. First, we propose an overall mapping flow for mapping algorithms onto the platform of REMUS-II system and then illustrate it by implementing the H.264 encoder. Second, parallel and pipelining techniques are considered for fully exploiting the abundant computing resources of REMUS-II, thus increasing total computing throughput and solving high computational complexity of H.264 encoder. Besides, some data-reuse schemes are also used to increase data-reuse ratio and therefore reduce the required data bandwidth. Third, we propose a scheduling scheme to manage run-time reconfiguration of the system. The scheduling is also responsible for synchronizing the data communication between tasks and handling conflict between hardware resources. Experimental results prove that the REMUS-MB (REMUS-II version for mobile applications) system can perform a real-time H.264/AVC baseline profile encoder. The encoder can encode CIF@30fps video sequences with two reference frames and maximum search range of [-16,15]. The implementation, thereby, can be applied to handheld devices targeted at mobile multimedia applications. The platform of REMUS-MB system is designed and synthesized by using TSMC 65nm low power technology. The die size of REMUS-MB is 13.97mm². REMUS-MB consumes, on average, about 100mW while working at 166MHz. To my knowledge, in the literature this is the first implementation of H.264 encoding algorithm on a coarse-grained dynamically reconfigurable computing system.