The in-flight instrumental background of the Follow-up X-ray Telescope (FXT) onboard Einstein Probe mission is analysed in this work by utilizing observations collected during the performance verification phase and subsequent dedicated filter wheel closed observations. The instrumental backgrounds of the two FXT modules are consistent with each other, with an average rate of ∼4 × 10−2 counts s−1 keV−1 in the 0.5–10 keV band for each module. The background is nearly uniformly distributed across the detector area, with a minor increase (<8%) observed along rows. The spatial distribution shows significant modulation by the geomagnetic field. The spectral shapes remain unchanged in 0.5–10 keV at different rates. The long-term temporal variation indicates a periodic change associated with the orbital precession (∼57 days). The innovative design of FXT full-frame readout mode enables simultaneous recording of events in both the imaging area (IMG) and the frame store area (FSA) of the pnCCD. FSA event rates show a strong linear correlation with the IMG, based on which the IMG instrumental background modeling is established.