Equation Modeling technique has not been fully utilized in the field of Software analysis in handling complex data analysis and modeling on programming languages by a number of researches globally and specifically by Universities in East Africa, in a nut shell; secures programming practices and daily life application is still wanting. We present a comparative study of C, C++, C#, and Java Programming languages: Underpinning Structure Equation Modeling; with respect to: Runtime tests, compilation, Model comparison, Latent Curve model, rate of change over time, Runtime tests, sorting criteria and compilation. Findings indicated that Java was: (Var_Inter =0.81 and Var_slop =0.02). The overall model fit for Java had (RMR =0.000, CFI = 9.88, TLI = 1.0, and NFI = 0.99), while that of C-language was poorly fitted, its Latent Curve model results: (Var-Inter =0.41 and Var_Slop =0.31) hence not significant. Rule of thumb utilized was excellent; Java was rated higher in terms of Runtime tests, same applied to sorting criteria; Merge sort, applicabilication and compilation, While C was the least. C++ gave close results to C, Comparatively C# had better finding. On sorting criteria, Java indicated a more coherent than a C++ and C, but closer to C#, Java was rated as more simplified, Java applications are more than the 3 languages. Study recommends further investigation on C and C++, all the same there is need to carry out research on more than four languages and to use a larger sample size.