diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index 80e5e89b79690..7060cdf79d6f7 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -546,6 +546,7 @@ I/O
 - Bug in :meth:`DataFrame.to_excel` when writing empty :class:`DataFrame` with :class:`MultiIndex` on both axes (:issue:`57696`)
 - Bug in :meth:`DataFrame.to_stata` when writing :class:`DataFrame` and ``byteorder=`big```. (:issue:`58969`)
 - Bug in :meth:`DataFrame.to_string` that raised ``StopIteration`` with nested DataFrames. (:issue:`16098`)
+- Bug in :meth:`HDFStore.get` was failing to save data of dtype datetime64[s] correctly (:issue:`59004`)
 - Bug in :meth:`read_csv` raising ``TypeError`` when ``index_col`` is specified and ``na_values`` is a dict containing the key ``None``. (:issue:`57547`)
 - Bug in :meth:`read_stata` raising ``KeyError`` when input file is stored in big-endian format and contains strL data. (:issue:`58638`)
 
diff --git a/pandas/io/pytables.py b/pandas/io/pytables.py
index 4fce338ccad6f..d98c51159eb63 100644
--- a/pandas/io/pytables.py
+++ b/pandas/io/pytables.py
@@ -2655,7 +2655,7 @@ def convert(self, values: np.ndarray, nan_rep, encoding: str, errors: str):
         # reverse converts
         if dtype.startswith("datetime64"):
             # recreate with tz if indicated
-            converted = _set_tz(converted, tz)
+            converted = _set_tz(converted, tz, dtype)
 
         elif dtype == "timedelta64":
             converted = np.asarray(converted, dtype="m8[ns]")
@@ -3036,7 +3036,7 @@ def read_array(self, key: str, start: int | None = None, stop: int | None = None
             if dtype and dtype.startswith("datetime64"):
                 # reconstruct a timezone if indicated
                 tz = getattr(attrs, "tz", None)
-                ret = _set_tz(ret, tz)
+                ret = _set_tz(ret, tz, dtype)
 
             elif dtype == "timedelta64":
                 ret = np.asarray(ret, dtype="m8[ns]")
@@ -4964,7 +4964,9 @@ def _get_tz(tz: tzinfo) -> str | tzinfo:
     return zone
 
 
-def _set_tz(values: npt.NDArray[np.int64], tz: str | tzinfo | None) -> DatetimeArray:
+def _set_tz(
+    values: npt.NDArray[np.int64], tz: str | tzinfo | None, datetime64_dtype: str
+) -> DatetimeArray:
     """
     Coerce the values to a DatetimeArray with appropriate tz.
 
@@ -4972,11 +4974,13 @@ def _set_tz(values: npt.NDArray[np.int64], tz: str | tzinfo | None) -> DatetimeA
     ----------
     values : ndarray[int64]
     tz : str, tzinfo, or None
+    datetime64_dtype : str, e.g. "datetime64[ns]", "datetime64[25s]"
     """
     assert values.dtype == "i8", values.dtype
     # Argument "tz" to "tz_to_dtype" has incompatible type "str | tzinfo | None";
     # expected "tzinfo"
-    dtype = tz_to_dtype(tz=tz, unit="ns")  # type: ignore[arg-type]
+    unit, _ = np.datetime_data(datetime64_dtype)  # parsing dtype: unit, count
+    dtype = tz_to_dtype(tz=tz, unit=unit)  # type: ignore[arg-type]
     dta = DatetimeArray._from_sequence(values, dtype=dtype)
     return dta
 
diff --git a/pandas/tests/io/pytables/test_read.py b/pandas/tests/io/pytables/test_read.py
index e33ddaf3b81f0..ba108370a4a92 100644
--- a/pandas/tests/io/pytables/test_read.py
+++ b/pandas/tests/io/pytables/test_read.py
@@ -317,3 +317,14 @@ def test_read_infer_string(tmp_path, setup_path):
         columns=Index(["a"], dtype="string[pyarrow_numpy]"),
     )
     tm.assert_frame_equal(result, expected)
+
+
+def test_hdfstore_read_datetime64_unit_s(tmp_path, setup_path):
+    # GH 59004
+    df_s = DataFrame(["2001-01-01", "2002-02-02"], dtype="datetime64[s]")
+    path = tmp_path / setup_path
+    with HDFStore(path, mode="w") as store:
+        store.put("df_s", df_s)
+    with HDFStore(path, mode="r") as store:
+        df_fromstore = store.get("df_s")
+    tm.assert_frame_equal(df_s, df_fromstore)
diff --git a/pandas/tests/io/pytables/test_round_trip.py b/pandas/tests/io/pytables/test_round_trip.py
index 51ee289c8e27a..3ad05cec3bca3 100644
--- a/pandas/tests/io/pytables/test_round_trip.py
+++ b/pandas/tests/io/pytables/test_round_trip.py
@@ -236,8 +236,10 @@ def test_table_values_dtypes_roundtrip(setup_path):
         df1["float322"] = 1.0
         df1["float322"] = df1["float322"].astype("float32")
         df1["bool"] = df1["float32"] > 0
-        df1["time1"] = Timestamp("20130101")
-        df1["time2"] = Timestamp("20130102")
+        df1["time_s_1"] = Timestamp("20130101")
+        df1["time_s_2"] = Timestamp("20130101 00:00:00")
+        df1["time_ms"] = Timestamp("20130101 00:00:00.000")
+        df1["time_ns"] = Timestamp("20130102 00:00:00.000000000")
 
         store.append("df_mixed_dtypes1", df1)
         result = store.select("df_mixed_dtypes1").dtypes.value_counts()
@@ -252,7 +254,9 @@ def test_table_values_dtypes_roundtrip(setup_path):
                 "int8": 1,
                 "int64": 1,
                 "object": 1,
-                "datetime64[ns]": 2,
+                "datetime64[s]": 2,
+                "datetime64[ms]": 1,
+                "datetime64[ns]": 1,
             },
             name="count",
         )