Freak waves are an extreme marine environment factor in offshore structure design and become a potential risk, particularly for laying oil-gas pipelines in deep waters. The objective of this study was to reveal the freak wave effects on dynamic behaviors of offshore pipelines for deepwater installation. Thus, a dedicated finite element model (FEM) for deepwater pipeline installation by the S-lay method was developed with special consideration of freak waves. The FEM also took pipelay vessel motions, pipe–stinger roller interactions, and the cyclic contacts between the pipeline and seabed soil into account. Real vessel and stinger data from an actual engineering project in the South China Sea were collected to obtain an accurate simulation. Moreover, an effective superposition approach of combined transient wave trains and random wave trains was introduced, and various types of freak wave trains were simulated. Extensive numerical analyses of a 12 inch gas pipeline being installed into a water depth of 1500 m were implemented under various freak wave conditions. The noticeable influences of freak waves on the pipeline and seabed responses were identified, which provides significant awareness of offshore pipelines for deepwater installation design and field operation monitoring.