There is disclosed a method and system for configuring a data dependency graph (DDG) to handle instruction scheduling in computer architectures permitting dynamic by-pass execution, and for performing dynamic by-pass scheduling utilizing such a configured DDG. In accordance with an embodiment of the invention, a heuristic function is used to obtain a ranking of nodes in the DDG after setting delays at all identified by-pass pairs of nodes in the DDG to 0. From among a list of identified by-pass pairs of nodes, a node that is identified as being the least important to schedule early is marked as “bonded” to its successor, and the corresponding delay for that identified node is set to 0. Node rankings are re-computed and the bonded by-pass pair of nodes are scheduled in consecutive execution cycles with a delay of 0 to increase the likelihood that a by-pass can be successfully taken during run-time execution.