diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1dec0c6741..a342da3fdc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,7 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+- Deprecated `pybamm.Simulation.set_parameters`, `pybamm.Simulation.set_up_and_parameterise_experiment` and `pybamm.Simulation.set_up_and_parameterise_model_for_experiment` functions in `pybamm.simulation.py`. ([#3752](https://github.com/pybamm-team/PyBaMM/pull/3752))
+
 ## Features
 
 - Added support for macOS arm64 (M-series) platforms. ([#3789](https://github.com/pybamm-team/PyBaMM/pull/3789))
diff --git a/pybamm/simulation.py b/pybamm/simulation.py
index aa58022b6d..4b6cb8efe3 100644
--- a/pybamm/simulation.py
+++ b/pybamm/simulation.py
@@ -186,6 +186,8 @@ def set_up_and_parameterise_experiment(self):
         This needs to be done here and not in the Experiment class because the nominal
         cell capacity (from the parameters) is used to convert C-rate to current.
         """
+        msg = "pybamm.simulation.set_up_and_parameterise_experiment is deprecated and not meant to be accessed by users."
+        warn(msg, DeprecationWarning)
         # Update experiment using capacity
         capacity = self._parameter_values["Nominal cell capacity [A.h]"]
         for op_conds in self.experiment.operating_conditions_steps:
@@ -216,6 +218,8 @@ def set_up_and_parameterise_model_for_experiment(self):
         This increases set-up time since several models to be processed, but
         reduces simulation time since the model formulation is efficient.
         """
+        msg = "pybamm.simulation.set_up_and_parameterise_model_for_experiment is deprecated not meant to be accessed by users."
+        warn(msg, DeprecationWarning)
         self.experiment_unique_steps_to_model = {}
         for op_number, op in enumerate(self.experiment.unique_steps):
             new_model = self._model.new_copy()
@@ -326,7 +330,8 @@ def set_parameters(self):
         """
         A method to set the parameters in the model and the associated geometry.
         """
-
+        msg = "pybamm.set_paramters is deprecated and not meant to be accessed by users."
+        warn(msg, DeprecationWarning)
         if self.model_with_set_params:
             return