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In many applications, multiple parties have private data regarding the same set of users but on disjoint sets of attributes, and a server wants to leverage the data to train a model. To enable model learning while protecting the privacy of the data subjects, we need vertical federated learning (VFL) techniques, where the data parties share only information for training the model, instead of the private data. However, it is challenging to ensure that the shared information maintains privacy while learning accurate models. To the best of our knowledge, the algorithm proposed in this paper is the first practical solution for differentially private vertical federated k-means clustering, where the server can obtain a set of global centers with a provable differential privacy guarantee. Our algorithm assumes an untrusted central server that aggregates differentially private local centers and membership encodings from local data parties. It builds a weighted grid as the synopsis of the global dataset based on the received information. Final centers are generated by running any k-means algorithm on the weighted grid. Our approach for grid weight estimation uses a novel, light-weight, and differentially private set intersection cardinality estimation algorithm based on the Flajolet-Martin sketch. To improve the estimation accuracy in the setting with more than two data parties, we further propose a refined version of the weights estimation algorithm and a parameter tuning strategy to reduce the final k-means utility to be close to that in the central private setting. We provide theoretical utility analysis and experimental evaluation results for the cluster centers computed by our algorithm and show that our approach performs better both theoretically and empirically than the two baselines based on existing techniques.