Fix Prometheus Stale NaN Timestamp Errors (2026)

Prometheus is failing to scrape targets because the timestamps it receives for metrics are invalid, specifically "NaN" (Not a Number).

Common Causes and Fixes:

1. Application Not Sending Timestamps Correctly:

   • Diagnosis: Check the application’s metrics endpoint. Look for metrics where the timestamp is explicitly NaN or missing. For example, if you can curl your application’s /metrics endpoint and see my_metric 123 NaN or my_metric{label="value"} NaN.
   • Fix: This is an application-level bug. The application code responsible for exposing metrics needs to be fixed to ensure it always sends a valid, monotonically increasing timestamp for each metric sample. This often involves ensuring your metrics library is configured correctly or that you’re not manually overriding timestamps with invalid values.
   • Why it works: Prometheus expects a numerical timestamp for every data point. NaN is not a number, so Prometheus rejects the sample, leading to staleness. Fixing the application ensures valid data is sent.

2. Clock Skew Between Prometheus Server and Target:

   • Diagnosis: On the Prometheus server, run date -u. On the target machine, run date -u. Compare the UTC timestamps. Significant differences (more than a few seconds) indicate clock skew.
   • Fix: Synchronize the clocks on both the Prometheus server and the target machine using NTP. On the target machine, ensure the ntpd or chronyd service is running and configured to sync with reliable time servers. For example, ensure /etc/ntp.conf or /etc/chrony/chrony.conf has valid server entries and the service is enabled: sudo systemctl enable --now ntp or sudo systemctl enable --now chronyd.
   • Why it works: Prometheus uses the timestamp sent by the target. If the target’s clock is wildly off, the timestamp it sends might appear invalid or nonsensical to Prometheus, especially if it’s in the far future or past relative to Prometheus’s own clock. NTP keeps clocks synchronized.

3. Network Latency Causing Timestamp Interpretation Issues:

   • Diagnosis: While less common for NaN, extremely high network latency or packet loss could theoretically lead to Prometheus receiving data with timestamps that are so far in the past they are considered invalid or stale by its internal logic, and in some edge cases, this might manifest as NaN if the underlying client library has a fallback. More commonly, you’d see "stale" targets or missed scrapes. However, if a custom exporter is involved, it might have peculiar error handling.
   • Fix: Optimize network paths between Prometheus and the target. Ensure sufficient bandwidth and low latency. For critical targets, consider deploying Prometheus closer to the targets or using a federated setup.
   • Why it works: Prometheus has internal tolerances for how far back a timestamp can be. If network issues cause a timestamp to arrive very late, it might be rejected.

4. Custom Exporter Bugs or Misconfiguration:

   • Diagnosis: If you’re using a custom-built exporter or one not maintained by a major project, inspect its code or configuration. Look for how it generates timestamps. A common mistake is using time.Now() directly in some languages without considering potential delays or using a fixed, incorrect timestamp in test scenarios.
   • Fix: Correct the timestamp generation logic in the custom exporter. Ensure it uses a reliable method for obtaining the current time and that this time is consistently formatted and sent.
   • Why it works: Similar to point 1, the exporter is the source of the bad data. Fixing it at the source resolves the issue.

5. Prometheus Server Time Synchronization Issues (Less Likely for NaN):

   • Diagnosis: Verify the Prometheus server’s clock is synchronized via NTP. date -u on the Prometheus server should be accurate.
   • Fix: Ensure NTP is running and correctly configured on the Prometheus server.
   • Why it works: While the target is the primary source of the timestamp, Prometheus uses its own clock for various internal checks, including staleness detection and determining if a timestamp is unreasonably old. If the Prometheus server’s clock is drastically wrong, its own rejection logic might be flawed.

6. Underlying Operating System or Hardware Issues on the Target:

   • Diagnosis: Check system logs (dmesg, /var/log/syslog) on the target machine for any hardware errors, kernel panics, or unusual system behavior that might affect timekeeping.
   • Fix: Address any underlying OS or hardware problems. This could involve driver updates, hardware replacement, or OS reinstallation.
   • Why it works: In rare cases, severe OS instability or hardware faults (like a failing RTC) can corrupt the system’s timekeeping, leading to bizarre timestamp values being reported by applications.

7. Bug in Prometheus Scraper or Remote Write Client:

   • Diagnosis: This is highly unlikely for NaN timestamps unless you are running a very old or a development version of Prometheus, or a custom remote write implementation. Check the Prometheus version (promtool --version). If using remote write, check the remote write client’s logs.
   • Fix: Upgrade Prometheus to the latest stable version. If using a custom remote write client, consult its documentation or source.
   • Why it works: Prometheus is generally robust in handling timestamps. A bug here would be a significant issue affecting many users.

The next error you’ll likely encounter, assuming the NaN timestamp issue is resolved, is related to scrape timeouts or connection refused errors if the underlying connectivity or target application is also unstable.