Abstract A robot-arm-based mobile HTS-SQUID NDE system was developed for inspection of advanced structures such as hydrogen fuel cell tanks. In order to realize stable operation of HTS-SQUID exposed in Earth’s field and robot arm’s noise without flux trapping, flux jumping and unlocking during motion, a new active magnetic shielding (AMS) technique using fluxgate was introduced. The high sensitive fluxgate, which could measure magnetic field of up to several 10 μT, was mounted near an HTS-SQUID gradiometer on the robot arm to measure the ambient noise and feed back its output to a compensation coil, which surrounded both SQUID and fluxgate to cancel the ambient noise around them. The AMS technique successfully enabled the HTS-SQUID gradiometer to be moved at 10 mm/s by the robot arm in unshielded environment without flux trapping, jumping and unlocking. Detection of hidden slots in multi-layer composite-metal structures imitating the fuel cell tank was demonstrated.