Polls officially closed at 4pm, but people in queues are still allowed to vote.
Museveni, who has been in power since 1986, is seeking a sixth elected. His main challenger is Bobi Wine, the 38-year-old pop star-turned-politician.
The president voted in Rushere town in western Uganda.
Earlier, there were reports biometric voter verification kits had failed to work in a number of polling stations.
Electoral Commission's spokesperson, Paul Bukenya, said they had received reports that some of the kits had malfunctioned.
The electronic devices are used to capture and verify details of voters before they can be issued with ballot papers.
Long queues were spotted in most polling stations visited by the BBC, although there were delays in delivery of voting materials at some stations.
