In a `shortcut-to-adiabaticity (STA) protocol, the counter-diabatic Hamiltonian, which suppresses the non-adiabatic transition of a reference `adiabatic trajectory, induces a quantum uncertainty of the work cost in the framework of quantum thermodynamics. Following a theory derived recently [Funo et al 2017 Phys. Rev. Lett. 118 100602], we perform an experimental measurement of the STA work statistics in a high-quality superconducting Xmon qubit. Through the frozen-Hamiltonian and frozen-population techniques, we experimentally realize the two-point measurement of the work distribution for given initial eigenstates. Our experimental statistics verify (i) the conservation of the average STA work and (ii) the equality between the STA excess of work fluctuations and the quantum geometric tensor.