Further delays were caused after the previous Delta IV launch, the maiden flight of the Heavy configuration, suffered a partial failure.

[13] After these launch attempts, the rocket's flight termination system batteries expired, requiring replacement.

[15] At launch, the satellite had a mass of 3,133 kilograms (6,907 lb), and an expected operational lifespan of ten years, although it carries fuel for longer.

In December 2007, GOES-13 was called up to provide coverage of the East Coast of the United States during an outage of GOES-12 due to a thruster leak.

It was also briefly activated in mid-May 2009 when GOES-12 developed another thruster problem, however, it did not need to take over operations, and was deactivated by the end of the month.

[6] In September 2019, NOAA confirmed that GOES-13 had been transferred to the U.S. Air Force after the two-year negotiation in order to fill a gap in forecasting requirements, but NOAA would continue operating the satellite on behalf of the U.S. Air Force for its remaining life span.

The noise gradually increased to the point at which the satellite was placed in standby mode on 24 September 2012 in order to allow engineers to diagnose the problem.

GOES-15 temporarily provided backup imagery for a short time, with GOES-14 being taken out of in-orbit storage and prepared to be a longer-term replacement including movement towards the 75.0° slot normally occupied by GOES-East.

On 22 May 2013, at 03:40 UTC, GOES-13 was apparently hit by a micrometeorite or orbital debris (MMOD) which caused it to lose track of the stars that it uses to maintain attitude.

[28] GOES-13 was scheduled to return to operational status at 15:45 UTC on 6 June 2013[29] However, that was delayed due to a Critical Weather Day and Tropical Storm Andrea.