diff --git a/doc/source/whatsnew/v2.0.0.rst b/doc/source/whatsnew/v2.0.0.rst
index 1c99ba0b8e412..f22940549e81c 100644
--- a/doc/source/whatsnew/v2.0.0.rst
+++ b/doc/source/whatsnew/v2.0.0.rst
@@ -1075,8 +1075,8 @@ Metadata
 
 Other
 ^^^^^
+- Add future warnings in :meth:`DataFrameGroupBy.fillna` and :meth:`SeriesGroupBy.fillna` allowing only keyword arguments to be passed except ``value`` (:issue:`48395`)
 - Bug in :meth:`Series.searchsorted` inconsistent behavior when accepting :class:`DataFrame` as parameter ``value`` (:issue:`49620`)
--
 
 .. ***DO NOT USE THIS SECTION***
 
diff --git a/pandas/core/groupby/generic.py b/pandas/core/groupby/generic.py
index 905c1193713cc..e560df1aa3cfd 100644
--- a/pandas/core/groupby/generic.py
+++ b/pandas/core/groupby/generic.py
@@ -48,6 +48,7 @@
 from pandas.util._decorators import (
     Appender,
     Substitution,
+    deprecate_nonkeyword_arguments,
     doc,
 )
 
@@ -788,6 +789,7 @@ def build_codes(lev_codes: np.ndarray) -> np.ndarray:
             out = ensure_int64(out)
         return self.obj._constructor(out, index=mi, name=self.obj.name)
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "value"])
     def fillna(
         self,
         value: object | ArrayLike | None = None,
@@ -2229,6 +2231,7 @@ def value_counts(
         """
         return self._value_counts(subset, normalize, sort, ascending, dropna)
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "value"])
     def fillna(
         self,
         value: Hashable | Mapping | Series | DataFrame = None,