Mr Horner, 35, was shot in a supermarket car park in front of his three-year-old son at Balloo Link, Bangor, on Sunday afternoon.
Police described his murder as "brutal, senseless and horrendous".
The man has also been charged with possession of a firearm and ammunition with intent to endanger life. He is to appear in court in Newtownards on Friday morning.
A 47-year-old man also arrested over the murder has been released unconditionally.
Det Supt Kevin Geddes thanked people who had come forward with "vital information".
He also appealed for anyone who may have footage of the scene from devices or dashcams, or has any other information, to get in touch.
The detective said he particularly wanted to hear from anyone who saw Mr Horner leave his partner's home at Balloo Road in Bangor in a black Nissan Pulsar - reg XFZ 4706 - at about 14:00 BST, until he arrived at Sainsbury's car park at about 14:30 BST.
Police also want to know about the movements of a red Ford Mondeo with false number plates - GKZ 7996 - which was last seen speeding from the scene at 14:50 BST. It was later found burnt out at Kerr's Road in Bangor.
The PSNI had previously said they were investigating a possible link between Mr Horner's murder and a loyalist paramilitary feud.
Police have charged a 28-year-old man with the murder of Colin Horner.