Resorting to a three-dimensional finite element framework, the paper investigates the instantaneous and long-term deformation in twin tunnels with connecting transverse gallery. Particular emphasis is dedicated to the assessment of combined effects induced by the time-dependent behavior of the constituent materials, twin tunnels proximity and tunnel junctions on the convergence profile. At the material level, the rock mechanical behavior is formulated within the context of coupled plasticity–viscoplasticity, which proves relevant for modeling the tunnel deformation in deep clayey rocks. As regards the time-dependent properties of the lining concrete, creep deformation is addressed by means of an aging viscoelastic model relying on the Bažant and Prasannan Solidification Theory, whereas the shrinkage deformation component is based on the formulation proposed in CEB-FIP MC90 standard. At the structure level, the deactivation-activation technique is employed in the three-dimensional finite element model to simulate the excavation/advancing face and lining installation processes. The accuracy of the approach is assessed by comparison of the model predictions with available analytical and numerical stress solutions derived in the context of simplified twin tunnel configurations. The three-dimensional computational model is then applied to analyze the deformation mechanisms in circular twin tunnels with a transverse gallery. The numerical simulations emphasized the significant deformation anisotropy induced by tunnels proximity, the peak convergence values observed at tunnel-gallery junction as well as the crucial role of time-dependent properties of concrete lining in controlling the tunnel deformation.