The Škoda CITIGO has been scrutinised by Euro NCAP and the car is structurally identical to the Volkswagen up! and has the same interior fittings. Škoda has informed Euro NCAP that the CITIGO also has the same levels of safety equipment as the up!. Accordingly, Euro NCAP believes that the star rating of the up! can also be applied to the Škoda CITIGO.

The passenger compartment remained stable in the frontal offset test. Dummy readings indicated good protection of the knees and femurs of the driver and passenger. It was shown that a similar level of protection would be provided to occupants of different sizes and to those sitting in different positions. Chest protection of both dummies was marginal. In the full-width rigid barrier test, protection of the chest was again marginal for both occupants, with other critical body areas well or adequately protected. In the side barrier impact, all critical body areas were well protected and the car scored maximum points in this test. In the more severe side pole test, protection of the chest was adequate and that of other body areas was good. Tests on the front seats and head restraints demonstrated good protection against whiplash injuries in the event of a rear-end collision. A geometric assessment of the rear seats indicated marginal whiplash protection. An autonomous emergency braking (AEB) system is not available.

In the frontal offset test, protection of the neck of the 10 year dummy was rated as marginal, based on dummy readings of tensile forces. Protection of the 6 year dummy was good. In the side barrier test, dummy readings of accelerations in the chest of the 10 year dummy indicated poor protection of that body area. The front passenger airbag can be disabled to allow a rearward-facing child restraint to be used in that seating position. Clear information if provided to the driver and the system was rewarded. All of the restraint types for which the car is designed could be properly installed and accommodated in the car.

The bonnet provided good or adequate protection to the head of a struck pedestrian over most of its surface but there were broad areas of poor performance along the base of the windscreen and on the stiff windscreen pillars. The bumper provided good protection to pedestrians' legs but protection of the pelvis was mixed.

The CITIGO has a seatbelt reminder system for the front and rear seats. A lane support system helps prevent inadvertent drifting out of lane and also intervenes in some more critical situations. A speed assistance system uses digital mapping to determine the local speed limit and presents this information to the driver.