In this era of digital transformation, startups in Indonesia have been developing faster than ever before. Every startup seeks to gain a competitive advantage through increased efficiency and predictability of their development processes. This paper aims to design the software development project using the Design Structure Matrix (DSM). The DSM methodology was used to capture unique features such as nested and planned iterations, which are inherent in agile projects like a software development project. The DSM model was analyzed using Monte Carlo simulation, which outputs sample cost and schedule outcome distributions captured in the Probability Density Function Graph to reveal opportunities to trade cost and schedule risk. A comparative analysis was also conducted between the schedule based on DSM and Simulation with a schedule based on the Critical Path Method (CPM). This research proved that DSM could manage design iteration or rework and is more effective in portraying an agile project than traditional project management tools like CPM. This case study was done at one of Indonesia’s emerging financial marketplace.