STS-99 faced a series of launch delays and one scrub before launching successfully. The mission was originally scheduled to fly on Sept. 16, 1999. But in mid-August, the launch date was postponed until October because of wiring concerns throughout the Shuttle fleet. With so much of Endeavour's wiring requiring inspection, the target date for launch was shifted to no earlier than Nov. 19. Shuttle managers later decided to preserve the option to launch either STS-99, or STS-103, the Third Hubble Servicing Mission, first. It was decided in October that STS-103 would fly first, and the launch of STS-99 was set for Jan. 13, 2000. In December that date came under review, and a new launch date of no earlier than Jan. 31 was set. The scheduled launch on Jan. 31, 2000, was scrubbed because of unacceptable weather conditions. However, late in the count, an anomaly occurred with the No. 2 enhanced master events controller (EMEC), which also would have prevented the launch on that day. The EMEC was removed and replaced and the launch rescheduled until 12:30 p.m. EST on Feb. 11. About three hours prior to the scheduled launch, an unexpected pressure drop was detected in hydraulic system 1. The pressure drop was determined to be the result of a normal sequence of prelaunch events. Discussions of the pressure drop resulted in a 13-minute, 40-second launch delay.

This launch sequence was photographed from the VAB roof.