The entrance to the park now welcomes guests with six American flags.
Flags were replaced Friday at Six Flags Over Texas, Six Flags Fiesta Texas and Six Flags Over Georgia, the only parks where the flags were flown.
Since it opened in 1961, Six Flags Over Texas has flown flags from all six nations to which the state belonged through its history - including the Confederate flag.
A day after announcing that no, it wouldn't remove the Confederate flag from the theme park's marquee, Six Flags Over Texas has decided that maybe it's a good idea.
Six Flags spokeswoman Sharon Parker said, "We always choose to focus on celebrating the things that unite us versus those that divide us".
Why was there a Confederate flag in the first place? However both flags flew during the Civil War.
Some threatened to cancel their season passes while others applauded the theme park chains for taking down the flags.
The Stars and Bars version, a name often misappropriated to the battle flag, has a field made up of three alternating red and white horizontal stripes with a blue square in the corner housing a ring of white stars. So Confederate officers appealed to for another banner, which prompted the Confederate Battle Flag most know about today, known as the "Southern Cross" plan.
"The fact is the Confederacy did exist and Texas was a part of it", Shannon Wynne said to the Fort Worth Star-Telegram.