The aircraft engine operates in various conditions. In consequence, the design of seals must take account of the seal clearance changes and the risk of rubbing. A small radial clearance of the rotor tip seal leads to the honeycomb rubbing in take-off conditions, and the leakage flow may increase in cruise conditions. The aim of this study is to compare two honeycomb seal configurations of the low-pressure gas turbine rotor. In the first configuration, the clearance is small and rubbing occurs. In the second,—the fins of the seal are shorter to eliminate rubbing. It is assumed that the real clearance in both configurations is the same. A study of the honeycomb geometrical model is performed to reduce the computational effort. The problem is investigated numerically using the RANS equations and the two-equation k–ω SST turbulence model. The honeycomb full structure is taken into consideration to show details of the fluid flow. Main parameters of the clearance and leakage flows are compared and discussed for the rotor different axial positions. An assessment of the leakage flow through the seal variants could support the design process.