TomoTools3D is a windows application software for imaging the seismic subsurface structure by travel time tomography. The program includes efficient tools to conduct a complete seismic tomography inversion, Constructing cross sections, and plotting. The tomography method used in this program is the Zhao et al. (1992, 1994) tomographic method. This version of the code is version 4.2 and adopted for the Windows OS and compiled using the Microsoft Visual Studio 2019 and Intel Visual Fortran. Tomotools3D User Guide is found in this dataset. System requirements: Win 10/11, 8.0 GB RAM at least. This copy of the software is optimized for the Research paper: “Tomographic Imaging of the Northern Red Sea Rift Structures: implications for the seismo-volcanic activity across the rift” The corresponding dataset is included. Here, we present the last version of the code (Tomotools3D V4.2) with all the requirements to conduct a complete tomography inversion and reproduce the results of this paper. This is the complete dataset of the seismic tomography imaging of the northern Red Sea rift Zone. The dataset includes the Tomotools3D V4.2 software and all the data required to reproduce the resulted images of this study. Detailed description of the software usage and the tomographic procedure are given in detail in the README-Tomography file. This program uses the seismic tomography code provided by Dapeng Zhao 1992, 1994 as the core of the tomography inversion. Additionally, windows interfaces, plotting and cross-section tools are added to maintain a flexible tomographic inversion in windows environment. For more information contact: mfarouk40@yahoo.com ; mfibrahim@kau.edu.sa ; dapeng.zhao.d2@tohoku.ac.jp