Public perception towards pipeline development and eminent domain concerns around pipeline routing represent a major obstacle in the implementation of carbon capture and sequestration (CCS) infrastructure. Previously, pipeline routing software and literature has focused on finding the least-cost path for routing pipelines. However, these methods often rely on incomplete information and cannot account for social issues such as negotiations with landowners or the complex cost-benefit analysis when considering alternative routing pathways. To address this, we develop and apply the k-shortest paths with limited overlap (kSPwLO) algorithm ESX to pipeline routing scenarios to provide many alternative paths and assess how these paths can inform practical pipeline development concerns. First, we apply the algorithm to a simple case of routing between one emissions source and one sequestration sink while adjusting the input parameter of the ESX algorithm. Next, we apply the algorithm to a complex network of sources and sinks to determine how alternate pipeline routes might impact the overall network structure, and we compare the costs of the alternate structure to the optimal solution provided by the SimCCSPRO CCS infrastructure design software. We find that the ESX algorithm efficiently and effectively finds alternate routing paths at a marginal increase in transportation cost (4.5–6.2%) when compared against the optimal route. We also find that many pipeline segments deploy intermittently across different routing simulations, indicating that, at the given cost uncertainty, many different solutions exist and network structure is often robust to changes in pipeline routing. We demonstrate that the ESX algorithm can be used to develop a cost-benefit analysis for choosing between multiple pipeline routes.