diff --git a/CHANGES b/CHANGES
index 6ce3e51f3..b12528a0a 100644
--- a/CHANGES
+++ b/CHANGES
@@ -58,6 +58,8 @@ Bugs fixed
 * #9878: mathjax: MathJax configuration is placed after loading MathJax itself
 * #9857: Generated RFC links use outdated base url
 * #9909: HTML, prevent line-wrapping in literal text.
+* #10061: html theme: Configuration values added by themes are not be able to
+  override from conf.py
 * #9925: LaTeX: prohibit also with ``'xelatex'`` line splitting at dashes of
   inline and parsed literals
 * #9944: LaTeX: extra vertical whitespace for some nested declarations
diff --git a/sphinx/config.py b/sphinx/config.py
index 38ed1d388..a4a448366 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -251,6 +251,17 @@ class Config:
             if name in self.values:
                 self.__dict__[name] = config[name]
 
+    def post_init_values(self) -> None:
+        """
+        Initialize additional config variables that are added after init_values() called.
+        """
+        config = self._raw_config
+        for name in config:
+            if name not in self.__dict__ and name in self.values:
+                self.__dict__[name] = config[name]
+
+        check_confval_types(None, self)
+
     def __getattr__(self, name: str) -> Any:
         if name.startswith('_'):
             raise AttributeError(name)
@@ -427,7 +438,7 @@ def check_confval_types(app: "Sphinx", config: Config) -> None:
                          "but `{current}` is given.")
                 logger.warning(msg.format(name=confval.name,
                                           current=confval.value,
-                                          candidates=annotations.candidates))
+                                          candidates=annotations.candidates), once=True)
         else:
             if type(confval.value) is type(default):
                 continue
@@ -452,13 +463,13 @@ def check_confval_types(app: "Sphinx", config: Config) -> None:
                     permitted = " or ".join(wrapped_annotations)
                 logger.warning(msg.format(name=confval.name,
                                           current=type(confval.value),
-                                          permitted=permitted))
+                                          permitted=permitted), once=True)
             else:
                 msg = __("The config value `{name}' has type `{current.__name__}', "
                          "defaults to `{default.__name__}'.")
                 logger.warning(msg.format(name=confval.name,
                                           current=type(confval.value),
-                                          default=type(default)))
+                                          default=type(default)), once=True)
 
 
 def check_primary_domain(app: "Sphinx", config: Config) -> None:
diff --git a/sphinx/theming.py b/sphinx/theming.py
index cfbe74b57..819cec377 100644
--- a/sphinx/theming.py
+++ b/sphinx/theming.py
@@ -208,6 +208,7 @@ class HTMLThemeFactory:
         try:
             entry_point = theme_entry_points[name]
             self.app.registry.load_extension(self.app, entry_point.module)
+            self.app.config.post_init_values()
             return
         except KeyError:
             pass