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The accurate and stable synchronization between electron bunch and external laser is a key requirement for the successful operation of an externally seeded free electron laser. This requirement is particularly stringent when the electron bunch is longitudinally compressed to sub-ps durations. We present an analytical description of the electron bunch arrival-time jitter that, supported by experimental evidence, allows the identification of specific, dominant jitter sources. The arrival-time jitter measurements were carried out as a function of the bunch length compression factor in FERMI@Elettra linac. The experimental behavior of the pulse-to-pulse time jitter agrees well both with the analytical predictions and particle tracking simulations. Our modeling takes into account the photoinjector laser arrival time on the cathode, the jitter of phases and voltages of the radio-frequency accelerator, and fluctuations of the compressor’s dipole field.