Context. Very Long Baseline Interferometry (VLBI) observations can resolve the radio structure of Active Galactic Nuclei (AGN) and provide estimates of the structural and kinematic characteristics at parsec-scales in their jets. The changes in the kinematics of the observed jet features can be used to study the physical conditions in the innermost regions of these sources. We performed multi-frequency multi-epoch Very Long Baseline Array (VLBA) observations of the blazar CTA102 during its 2006 radio flare, the strongest ever reported for this source. These observations provide an excellent opportunity to investigate the evolution of the physical properties of blazars, especially during these flaring events Aims. We want to study the kinematic changes in the source during the strong radio outburst in April 2006 and test the assumption of a shock-shock interaction. This assumption is based on the analysis and modeling of the single dish observations of CTA102 (Paper I). Methods. In this paper we study the kinematics of CTA102 at several frequencies using VLBI observations. From the modeled jet features we derive estimates on the evolution of the physical parameters, such as the particle density and the magnetic field. Furthermore, we combine our observations during the 2006 flare with long-term VLBA monitoring of the source at 15 GHz and 43 GHz. Results. We cross-identified seven features throughout our entire multifrequency observations and find evidence of two possible recollimation shocks around 0.1   mas (deprojected 18 pc at a viewing angle ϑ = 2.6°) and 6.0   mas (deprojected 1 kpc) from the core. The 43   GHz observations reveal a feature ejected at epoch tej = 2005.9 ± 0.2, which could be connected to the 2006 April radio flare. Furthermore, this feature might be associated with the traveling component involved in the possible shock-shock interaction, which gives rise to the observed double peak structure in the single-dish light curves reported in Paper I.