Geotechnical engineering problems are always faced with various sources of uncertainty, especially the uncertainties of soil properties. This paper presents the seismic fragility analysis of free-spanning submarine pipelines (FSSPs) with consideration of soil spatial variability. Firstly, the two-dimensional random field theory is employed to account for the spatial distribution characteristics of soil properties, and the levels of spatial variability are shifted by changing the autocorrelation lengths. Then, based on the generated random field data, the finite element (FE) models of the soil-pipe system are established and the offshore spatial motions applied to pipelines are stochastically synthesized. Meanwhile, the impacts of soil spatial variability on the soil-pipe interaction and offshore motion propagation are investigated. Next, the probabilistic seismic demand models of FSSPs are derived via dynamic analyses and statistical regression, and the seismic fragility curves are generated. The influence of soil spatial variability on the seismic performance of FSSPs is examined by comparing the fragility curves between the random-field and random-variable cases. Finally, a fast assessment method for the ultimate bearing capacity is proposed to simply incorporate soil spatial variability in the seismic performance estimation of FSSPs. Numerical results highlight the necessity of incorporating soil spatial variability in seismic fragility analysis of FSSPs. The proposed assessment method can provide a great convenience for designers and engineers to obtain the accurate ultimate bearing capacity of FSSPs or other underground structures in the preliminary stage of seismic design.