The rocket was launched just before 10 a.m. Korean time (0100 GMT) and overflew the Japanese island of Okinawa. Its April rocket launch was aborted after less than two minutes flight.
Both South Korea and Japan called meetings of their top security councils after the launch. Japanese television station NHK said the second stage of the rocket had crashed into seas off the Philippines as planned.
It was not immediately clear if the third stage carrying the satellite had made it into space.
There was no immediate annoucement from North Korea on the launch. It made a formal announcement when the April launch had failed, but has previously claimed that it put a satellite into space in 2009, something no one has been able to verify.
"We will convene an emergency security meeting at 10:30. The launch was made around 9.50 a.m.," an official at South Korea's presidential office in Seoul said.
The North launched the rocket close to the first anniversary of the death of former leader Kim Jong-il and as elections loom in South Korea and Japan.
Pyongyang says it is entitled to launch a satellite into space but critics say the rocket development is aimed at nurturing the kind of technology needed to mount a nuclear warhead on a long-range missile.
North Korea is banned from conducting missile and nuclear-related tests under U.N. sanctions imposed after its 2006 and 2009 nuclear tests.
The rocket's path was scheduled to pass between the Korean peninsula and China, with a second stage splashing down off the Philippines before launching the satellite into orbit.
Most political analysts believe the launch is designed to bolster the credentials of new leader Kim Jong-un as he cements his rule over the country of 22 million people.
A government official in Seoul said recently that the transition of power to Kim Jong-un did not appear to be going as smoothly as anticipated and there were signs that the regime was concerned over the possibility of rising dissent.
Kim is the third of his line to rule North Korea, whose national output is around one-fortieth of that of prosperous South Korea.
Plans for the launch had drawn criticism from South Korea, Russia, Japan and the United States as well as NATO and the United Nations.
The North's only major diplomatic ally, China, has expressed "deep concern" over the launch but is thought unlikely to back any further sanctions against its ally.