The problem of architecting a reliable transport system across an overlay network using split TCP connections as the transport primitive is mainly considered. The considered overlay network uses the application-level switch in each intermediate host. We first argue that natural designs based on store-and-forward principles that are maintained by split TCP connections of hop-by-hop approaches. These approaches in overlay networks do not concern end-to-end TCP semantics. Then, a new transport protocol-Overlay Transport Protocol (OTP)-that manages the end-to-end connection and is responsible for the congestion/flow control between source host and destination host is proposed. The proposed network model for the congestion and flow control mechanisms uses a new window size-Ownd-and a new timer in the source host and destination host. We validate our analytical findings and evaluate the performance of our OTP using a prototype implementation via simulation.