Preface
As shown in the picture, my GitHub notification logo always has a blue dot indicator, but when I click it, there is nothing there.

Solution
After submitting an issue on GitHub, someone quickly helped. I’ll write down the solution first and explain the reason later.
- First, create a token and select the notification permission,
- Then open the GitHub notifications page, open the browser developer mode (
F12orCtrl+Shift+I), and open the console in the terminal,

Paste this code into the console and press Enter:
const token = "Paste the token you just created here";
fetch('https://api.github.com/notifications', {
method: 'PUT',
headers: {
'Accept': 'application/vnd.github+json',
'Authorization': `Bearer ${token}`
},
body: JSON.stringify({}) // An empty body marks all notifications as read.
}).then(response => {
if (response.status === 205) {
console.log('✅ Success! The small blue dot on the notification logo should have disappeared, you can delete the token now.');
} else {
console.error('❌ Request failed. Status:', response.status);
response.json().then(data => console.error('Error details:', data));
}
}).catch(error => console.error('Bummer, there was a network error:', error));
Cause analysis
That blue dot in the inbox means GitHub thinks you still have an unread notification. If the notification itself has been cleared or the related issue was deleted, the counter can sometimes get stuck.
The simplest way to reset it is to open your notifications page and click Mark all as read in the top right. That clears the unread state across all repos. If the dot goes away after refreshing, the issue was just a stale entry.