Combating money laundering has become increasingly complex with the rise of cybercrime and digitalization of financial transactions. Graph-based machine learning techniques have emerged as promising tools for Anti-Money Laundering (AML) detection, capturing intricate relationships within money laundering networks. However, the effectiveness of AML solutions is hindered by data silos within financial institutions, limiting collaboration and overall efficacy. This research presents a novel privacy-preserving approach for collaborative AML machine learning, facilitating secure data sharing across institutions and borders while preserving privacy and regulatory compliance. Leveraging Fully Homomorphic Encryption (FHE), computations are directly performed on encrypted data, ensuring the confidentiality of financial data. Notably, FHE over the Torus (TFHE) was integrated with graph-based machine learning using Zama Concrete ML. The research contributes two key privacy-preserving pipelines. First, the development of a privacy-preserving Graph Neural Network (GNN) pipeline was explored. Optimization techniques like quantization and pruning were used to render the GNN FHE-compatible. Second, a privacy-preserving graph-based XGBoost pipeline leveraging Graph Feature Preprocessor (GFP) was successfully developed. Experiments demonstrated strong predictive performance, with the XGBoost model consistently achieving over 99% accuracy, F1-score, precision, and recall on the balanced AML dataset in both unencrypted and FHE-encrypted inference settings. On the imbalanced dataset, the incorporation of graph-based features improved the F1-score by 8%. The research highlights the need to balance the trade-off between privacy and computational efficiency.