Andrew Schneck, 25, was charged with attempting to maliciously damage or destroy the monument to Richard Dowling, a lieutenant in the Confederate army.
He was caught kneeling by it on Saturday with two boxes, duct tape, wires and a bottle containing liquids that could be used to make explosives, prosecutors said.
The 112-year-old statue is of Dowling in his Confederate uniform and guards the entrance to Hermann Park.
It stands on a pedestal inscribed with the names of anti-union soldiers who took part in the Battle of Sabine Pass, a key conflict in the American Civil War.
Mr Schneck, from Texas, was on five years’ probation after pleading guilty in 2014 to improperly storing explosive material.
His lawyer declined to comment on the latest arrest.
Civil rights activists have been ramping up calls for statues of Confederate leaders in the US to be removed.
The drive came to a head earlier this month when they clashed with KKK members and neo-Nazis rallying to save one dedicated to general Robert E Lee in Charlottesville.
The movement to take down Confederate statues has been criticised by President Donald Trump.
He tweeted last week: “Sad to see the history and culture of our great country being ripped apart with the removal of our beautiful statues and monuments.”