diff --git a/browser/ui/sidebar/sidebar_browsertest.cc b/browser/ui/sidebar/sidebar_browsertest.cc
index 47d26dbf737..af158ebe9bd 100644
--- a/browser/ui/sidebar/sidebar_browsertest.cc
+++ b/browser/ui/sidebar/sidebar_browsertest.cc
@@ -10,6 +10,7 @@
 #include "brave/browser/ui/sidebar/sidebar_service_factory.h"
 #include "brave/browser/ui/sidebar/sidebar_utils.h"
 #include "brave/browser/ui/views/frame/brave_browser_view.h"
+#include "brave/browser/ui/views/side_panel/brave_side_panel.h"
 #include "brave/browser/ui/views/sidebar/sidebar_container_view.h"
 #include "brave/browser/ui/views/sidebar/sidebar_control_view.h"
 #include "brave/browser/ui/views/sidebar/sidebar_items_contents_view.h"
@@ -88,10 +89,22 @@ class SidebarBrowserTest : public InProcessBrowserTest {
     sidebar_items_contents_view->OnItemPressed(item, event);
   }
 
+  SidebarControlView* GetSidebarControlView() const {
+    return GetSidebarContainerView()->sidebar_control_view_;
+  }
+
+  SidebarContainerView* GetSidebarContainerView() const {
+    return static_cast<SidebarContainerView*>(controller()->sidebar());
+  }
+
+  BraveSidePanel* GetSidePanel() const {
+    return GetSidebarContainerView()->side_panel_;
+  }
+
   bool IsSidebarUIOnLeft() const {
-    auto* sidebar_container_view =
-        static_cast<SidebarContainerView*>(controller()->sidebar());
-    return sidebar_container_view->sidebar_on_left_;
+    return GetSidebarContainerView()->sidebar_on_left_ &&
+           !GetSidePanel()->IsRightAligned() &&
+           GetSidebarControlView()->sidebar_on_left_;
   }
 };
 
@@ -227,6 +240,26 @@ IN_PROC_BROWSER_TEST_F(SidebarBrowserTest, IterateBuiltInWebTypeTest) {
   EXPECT_EQ(0, tab_model()->active_index());
 }
 
+// Test sidebar's initial horizontal option is set properly.
+IN_PROC_BROWSER_TEST_F(SidebarBrowserTest, PRE_InitialHorizontalOptionTest) {
+  auto* prefs = browser()->profile()->GetPrefs();
+
+  // Check default horizontal option is left-sided.
+  EXPECT_FALSE(prefs->GetBoolean(prefs::kSidePanelHorizontalAlignment));
+  EXPECT_TRUE(IsSidebarUIOnLeft());
+
+  // Set right-sided for next testing.
+  prefs->SetBoolean(prefs::kSidePanelHorizontalAlignment, true);
+}
+
+IN_PROC_BROWSER_TEST_F(SidebarBrowserTest, InitialHorizontalOptionTest) {
+  auto* prefs = browser()->profile()->GetPrefs();
+
+  // Check horizontal option is right-sided.
+  EXPECT_TRUE(prefs->GetBoolean(prefs::kSidePanelHorizontalAlignment));
+  EXPECT_FALSE(IsSidebarUIOnLeft());
+}
+
 IN_PROC_BROWSER_TEST_F(SidebarBrowserTest, EventDetectWidgetTest) {
   auto* widget = GetEventDetectWidget();
   auto* service = SidebarServiceFactory::GetForProfile(browser()->profile());
diff --git a/browser/ui/views/frame/brave_browser_view.cc b/browser/ui/views/frame/brave_browser_view.cc
index 7b27c33b297..94b3252131f 100644
--- a/browser/ui/views/frame/brave_browser_view.cc
+++ b/browser/ui/views/frame/brave_browser_view.cc
@@ -211,7 +211,6 @@ BraveBrowserView::BraveBrowserView(std::unique_ptr<Browser> browser)
         prefs::kSidePanelHorizontalAlignment,
         base::BindRepeating(&BraveBrowserView::OnPreferenceChanged,
                             base::Unretained(this)));
-    UpdateSideBarHorizontalAlignment();
   }
 }
 
@@ -266,6 +265,7 @@ sidebar::Sidebar* BraveBrowserView::InitSidebar() {
   // Start Sidebar UI initialization.
   DCHECK(sidebar_container_view_);
   sidebar_container_view_->Init();
+  UpdateSideBarHorizontalAlignment();
   return sidebar_container_view_;
 }
 
diff --git a/browser/ui/views/sidebar/sidebar_container_view.cc b/browser/ui/views/sidebar/sidebar_container_view.cc
index c656e4564df..5b3a8c7959d 100644
--- a/browser/ui/views/sidebar/sidebar_container_view.cc
+++ b/browser/ui/views/sidebar/sidebar_container_view.cc
@@ -125,18 +125,16 @@ void SidebarContainerView::Init() {
   // Hide by default. Visibility will be controlled by show options later.
   DoHideSidebar(false);
   UpdateToolbarButtonVisibility();
-  SetSidebarOnLeft(sidebar_on_left_);
 }
 
 void SidebarContainerView::SetSidebarOnLeft(bool sidebar_on_left) {
+  DCHECK(initialized_);
+
   if (sidebar_on_left_ == sidebar_on_left)
     return;
 
   sidebar_on_left_ = sidebar_on_left;
 
-  if (!initialized_)
-    return;
-
   DCHECK(sidebar_control_view_);
   sidebar_control_view_->SetSidebarOnLeft(sidebar_on_left_);
   GetEventDetectWidget()->SetSidebarOnLeft(sidebar_on_left_);