The structural and physical properties of Y5Ir6Sn18 grown from Sn-flux as large single crystals are studied. Y5Ir6Sn18 crystallizes with a unique structure [space group Fm3̄m, a = 13.7706(1) Å], which is characterized by a strong disorder. A transmission electron microscopy (TEM) study indicated that the structural model of Y5Ir6Sn18 obtained from X-ray diffraction methods is an average description of a complex intergrowth of domains with different structural arrangements. The studied stannide is a type-II superconductor with a critical temperature Tc = 2.1 K, a rather weak electron-phonon coupling and conventional s-wave BCS-like mechanisms. Performed theoretical electronic band structure calculations indicated the inconsistency of an idealized structural model earlier reported for Y5Ir6Sn18.