You can do it using the system identification app: https://www.mathworks.com/help/ident/ref/systemidentification-app.html. For this, you also need the toolbox: https://www.mathworks.com/help/ident/index.html
Update by Kishen Mahadevan at MathWorks on 6/19/2024
Considering that the end goal here is to identify plant model (transfer function) for PID tuning, you can also directly use the PID Tuner app from Controls System Toolbox that lets you automatically tune the gains of PID controller for your plant model, including identifying new plant model from response data all within the same app. Identifying new plant model step requires System Identification Toolbox to obtain a plant from measured or simulated system response data.
Please refer to this page for more information on PID tuner - Tune PID controllers - MATLAB (mathworks.com)
Please refer to this example to see how to Interactively Estimate Plant Parameters from Response Data and tune PID controller gains - Interactively Estimate Plant Parameters from Response Data - MATLAB & Simulink (mathworks.com)
