diff --git a/jdaviz/configs/imviz/plugins/tools.py b/jdaviz/configs/imviz/plugins/tools.py
index 4dfa4d08d5..44121d477a 100644
--- a/jdaviz/configs/imviz/plugins/tools.py
+++ b/jdaviz/configs/imviz/plugins/tools.py
@@ -8,6 +8,7 @@
 from glue_jupyter.utils import debounced
 
 from jdaviz.core.tools import BoxZoom, PanZoom, _MatchedZoomMixin
+from jdaviz.configs.imviz.helper import get_top_layer_index
 
 __all__ = []
 
@@ -37,15 +38,18 @@ def deactivate(self):
 
     def on_click(self, data):
         # Find visible layers
-        visible_layers = [layer for layer in self.viewer.state.layers if layer.visible]
-        if len(visible_layers) == 0:
+        try:
+            i = get_top_layer_index(self.viewer)
+        except IndexError:
+            return
+        if i is None:
             return
 
         # Same data as mousemove event in Imviz viewer.
         # Any other config that wants this functionality has to have the following:
         #   viewer._get_real_xy()
         #   viewer.center_on() --> inherited from AstrowidgetsImageViewerMixin
-        image = visible_layers[0].layer
+        image = self.viewer.state.layers[i].layer
         x = data['domain']['x']
         y = data['domain']['y']
         if x is None or y is None:  # Out of bounds
diff --git a/jdaviz/configs/imviz/plugins/viewers.py b/jdaviz/configs/imviz/plugins/viewers.py
index a36e317caa..285d801b77 100644
--- a/jdaviz/configs/imviz/plugins/viewers.py
+++ b/jdaviz/configs/imviz/plugins/viewers.py
@@ -135,12 +135,12 @@ def blink_once(self, reversed=False):
     def on_limits_change(self, *args):
         try:
             i = get_top_layer_index(self)
-            if i is None:
-                return
         except IndexError:
             if self.compass is not None:
                 self.compass.clear_compass()
             return
+        if i is None:
+            return
         self.set_compass(self.state.layers[i].layer)
 
     @property
diff --git a/jdaviz/configs/imviz/tests/test_tools.py b/jdaviz/configs/imviz/tests/test_tools.py
index dd260f800e..4d6abab8af 100644
--- a/jdaviz/configs/imviz/tests/test_tools.py
+++ b/jdaviz/configs/imviz/tests/test_tools.py
@@ -1,7 +1,10 @@
 import numpy as np
+import pytest
+from astropy.coordinates import SkyCoord
+from astropy.nddata import NDData
 from numpy.testing import assert_allclose
 
-from jdaviz.configs.imviz.tests.utils import BaseImviz_WCS_WCS
+from jdaviz.configs.imviz.tests.utils import BaseImviz_WCS_WCS, create_example_gwcs
 
 
 class TestPanZoomTools(BaseImviz_WCS_WCS):
@@ -64,6 +67,46 @@ def test_panzoom_tools(self):
         t_linkedpan.deactivate()
 
 
+@pytest.mark.parametrize("link_type", ["Pixels", "WCS"])
+def test_panzoom_click_center_linking(imviz_helper, link_type):
+    """https://github.com/spacetelescope/jdaviz/issues/2749"""
+    v = imviz_helper.default_viewer._obj
+
+    # Since we are not really displaying, need this to test pan/zoom.
+    v.shape = (100, 100)
+    v.state._set_axes_aspect_ratio(1)
+
+    arr_big = np.ones((40, 30), dtype=int)
+    w_big = create_example_gwcs(arr_big.shape)
+    arr_small = np.ones((20, 15), dtype=int)
+    w_small = create_example_gwcs(arr_small.shape)
+
+    imviz_helper.load_data(NDData(arr_big, wcs=w_big), data_label="big")
+    imviz_helper.load_data(NDData(arr_small, wcs=w_small), data_label="small")
+
+    lc_plugin = imviz_helper.plugins['Orientation']
+    lc_plugin.link_type = link_type
+
+    coo = SkyCoord(ra=197.89262754541807, dec=-1.3644568140486624, unit="deg")
+
+    if link_type == "WCS":
+        mouseover_loc = v.state.reference_data.coords.world_to_pixel(coo)
+    else:  # Pixels
+        mouseover_loc = w_small.world_to_pixel(coo)
+
+    t = v.toolbar.tools['jdaviz:imagepanzoom']
+    t.activate()
+    t.on_click({'event': 'click', 'domain': {'x': mouseover_loc[0], 'y': mouseover_loc[1]}})
+    t.deactivate()
+
+    # We want to make sure click centers viewer to where it is supposed to be.
+    cur_cen = v._get_center_skycoord()
+    v.center_on(coo)
+    real_cen = v._get_center_skycoord()
+    assert_allclose(cur_cen.ra.deg, real_cen.ra.deg)
+    assert_allclose(cur_cen.dec.deg, real_cen.dec.deg)
+
+
 def test_blink(imviz_helper):
     viewer = imviz_helper.default_viewer._obj