diff --git a/fs/config/ui.go b/fs/config/ui.go
index 1a897aefe..ab2163e6e 100644
--- a/fs/config/ui.go
+++ b/fs/config/ui.go
@@ -9,6 +9,7 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"regexp"
 	"slices"
 	"sort"
 	"strconv"
@@ -441,7 +442,7 @@ func backendConfig(ctx context.Context, name string, m configmap.Mapper, ri *fs.
 				out.Option.Examples[1].Value == "false" &&
 				out.Option.Exclusive {
 				// Use Confirm for Yes/No questions as it has a nicer interface=
-				fmt.Println(out.Option.Help)
+				fmt.Println(renderHelpForTerminal(out.Option.Help))
 				in.Result = fmt.Sprint(Confirm(Default))
 			} else {
 				value := ChooseOption(out.Option, name)
@@ -483,12 +484,26 @@ func RemoteConfig(ctx context.Context, name string) error {
 	return PostConfig(ctx, name, m, ri)
 }
 
+// rootRelativeMarkdownLink matches a markdown link with a root-relative
+// target, e.g. [encoding section in the overview](/overview/#encoding).
+var rootRelativeMarkdownLink = regexp.MustCompile(`\[([^\]]+)\]\((/[^)]*)\)`)
+
+// renderHelpForTerminal makes an option's help string readable on the
+// terminal. The same help text is also used to generate the website
+// documentation, where markdown links with root-relative targets resolve
+// correctly. On the terminal those links are confusing, so rewrite them to
+// "text (https://rclone.org/path)" using rclone.org as the implied root.
+func renderHelpForTerminal(help string) string {
+	return rootRelativeMarkdownLink.ReplaceAllString(help, "$1 (https://rclone.org$2)")
+}
+
 // ChooseOption asks the user to choose an option
 func ChooseOption(o *fs.Option, name string) string {
 	fmt.Printf("Option %s.\n", o.Name)
 	if o.Help != "" {
 		// Show help string without empty lines.
 		help := strings.ReplaceAll(strings.TrimSpace(o.Help), "\n\n", "\n")
+		help = renderHelpForTerminal(help)
 		fmt.Println(help)
 	}
 
diff --git a/fs/config/ui_internal_test.go b/fs/config/ui_internal_test.go
new file mode 100644
index 000000000..0f125db15
--- /dev/null
+++ b/fs/config/ui_internal_test.go
@@ -0,0 +1,45 @@
+package config
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestRenderHelpForTerminal(t *testing.T) {
+	for _, test := range []struct {
+		name string
+		help string
+		want string
+	}{
+		{
+			name: "no link",
+			help: "The encoding for the backend.",
+			want: "The encoding for the backend.",
+		},
+		{
+			name: "root relative link",
+			help: "See the [encoding section in the overview](/overview/#encoding) for more info.",
+			want: "See the encoding section in the overview (https://rclone.org/overview/#encoding) for more info.",
+		},
+		{
+			name: "root relative link without anchor",
+			help: "See [rclone serve sftp](/commands/rclone_serve_sftp) for details.",
+			want: "See rclone serve sftp (https://rclone.org/commands/rclone_serve_sftp) for details.",
+		},
+		{
+			name: "multiple links",
+			help: "[the time option docs](/docs/#time-options) and [authentication docs](/azureblob#authentication).",
+			want: "the time option docs (https://rclone.org/docs/#time-options) and authentication docs (https://rclone.org/azureblob#authentication).",
+		},
+		{
+			name: "absolute url left untouched",
+			help: "See [rclone forum](https://forum.rclone.org/) for help.",
+			want: "See [rclone forum](https://forum.rclone.org/) for help.",
+		},
+	} {
+		t.Run(test.name, func(t *testing.T) {
+			assert.Equal(t, test.want, renderHelpForTerminal(test.help))
+		})
+	}
+}