To comprehensively assess fractionated spacecraft, an assessment tool is developed based on lifecycle simulation under uncertainty driven by modular evolutionary stochastic models. First, fractionated spacecraft nomenclature and architecture are clarified, and assessment criteria are analyzed. The mean and standard deviation of risk adjusted lifecycle cost and net present value (NPV) are defined as assessment metrics. Second, fractionated spacecraft sizing models are briefly described, followed by detailed discussion on risk adjusted lifecycle cost and NPV models. Third, uncertainty sources over fractionated spacecraft lifecycle are analyzed and modeled with probability theory. Then the chronological lifecycle simulation process is expounded, and simulation modules are developed with object oriented methodology to build up the assessment tool. The preceding uncertainty models are integrated in these simulation modules, hence the random object status can be simulated and evolve with lifecycle timeline. A case study to investigate the fractionated spacecraft for a hypothetical earth observation mission is carried out with the proposed assessment tool, and the results show that fractionation degree and launch manifest have great influence on cost and NPV, and generally fractionated spacecraft is more advanced than its monolithic counterpart under uncertainty effect. Finally, some conclusions are given and future research topics are highlighted.