Yes. Assuming you have a command line application (i.e. you have a console application) that does not require user interaction, you can try the following in your controller method.
Process serverSideProcess = new Process();
serverSideProcess.StartInfo.FileName = @"C:\pathToTheExe";
serverSideProcess.StartInfo.Arguments = "arg1 arg2 arg3";
serverSideProcess.EnableRaisingEvents = true;
serverSideProcess.StartInfo.UseShellExecute = true;
serverSideProcess.Start();
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