Although endosseous implants are widely used in the clinic, failures still occur and their clinical performance depends on the quality of osseointegration phenomena at the bone-implant interface (BII), which are given by bone ingrowth around the BII. The difficulties in ensuring clinical reliability come from the complex nature of this interphase related to the implant surface roughness and the presence of a soft tissue layer (non-mineralized bone tissue) at the BII. The aim of the present study is to develop a method to assess the soft tissue thickness at the BII based on the analysis of its ultrasonic response using a simulation based-convolution neural network (CNN). A large-annotated dataset was constructed using a two-dimensional finite element model in the frequency domain considering a sinusoidal description of the BII. The proposed network was trained by the synthesized ultrasound responses and was validated by a separate dataset from the training process. The linear correlation between actual and estimated soft tissue thickness shows excellent R2 values equal to 99.52% and 99.65% and a narrow limit of agreement corresponding to [ -2.56, 4.32 μm] and [ -15.75, 30.35 μm] of microscopic and macroscopic roughness, respectively, supporting the reliability of the proposed assessment of osseointegration phenomena.