Negative Emissions Technologies (NETs) are now necessary solutions for climate change mitigation. NET portfolios that recommend a technology mix of individual NETs at smaller scales are preferred to ease their implementation's environmental and social impact. Resource constraints using the Planetary Boundaries as a framework can be used to ensure that the multi-footprints of NETs are within the planet’s safe operating space. However, for regional-scale applications, the uncertain resource constraints may highly depend on local conditions and the decisionmaker. There is a lack of studies investigating the effect of uncertain resource constraints on NET portfolios. This work addresses the research gap by applying a global sensitivity analysis using a space-filling Design of Experiments (DOE) strategy. First, a fuzzy, multi-period non-linear mathematical programming model is formulated. Computer experiments using a Latin hypercube space-filling DOE and regression analysis are then performed to investigate the effects of the varying resource constraints on the optimum NET portfolio. This approach enables the investigation of interactions and higher order effects of the parameters on the responses, the total negative emission potential and net present value of the portfolio, and the generation of response surface graphs, which are not available using traditional sensitivity analysis. The approach is demonstrated using a case study in the Association of Southeast Asian Nations region.