- An additional scene added straght in at the beginning immediately after the opening titles (originally it faded to the dig at giza) shows the entirety of the scene where Ra takes over the body of the caveboy showing the cavemen running from the light in the sky and showing him walking towards it. From this point it fades to the original opening scene at the Giza dig.
- Moments after the stargate has been hoisted up by the workmen at the Giza dig, people notice that there is something underneath it: a group of the Hora guards encased in the stone. The director's commentary on the DVD states that these are other guards that have come through the gate after it was sealed and were re-integrated straight into the stone.
- In the scene after the stargate has been opened for the first time and the military are checking the pictures of the marking of the gate on the other gate, after James Spader says he is 'positive' he can decipher the symbols, Kurt Russel's character turns and says "it's your call" in the theatrical version. In the special edition the line has been re-dubbed by him saying instead now "he's full of shit" - presumably this was done for rating purposes of the theatrical release.
- An additional scene before Kurt Russell is gearing up with the group about to go through the stargate, shows him going to a secured area to look at the stone/fossil Hora's.
- When the army group are setting up the camp in the desert there is a longer scene where the group discuss more about how the stargate works and how they are going to get back to Earth. The scene during the sandstorm inside the pyramid is also extended with more footage of them talking about the sandstorm and how they are going to get back to earth.
- When the sandstorm initially hits at the nagada village and Kurt Russell, James Spader and the others are locked inside the city, they decide that they do not want to stay and decide to leave; when the natives try to stop them Kurt Russell shoots at the ground to frightem them off. The boy (whom he later befriends) takes him up above to see the sandstorm approach. After this, a native that they were holding at gunpoint is released and Jackson comments "Sandstorm, that would have been a brilliant reason to shoot everyone".
- The scene when James Spader awakes in the sarcophagus after being killed is extended, showing him walking towards Ra's chamber, seeing a cat sitting on Ra's throne.
- When James Spader turns and shoots at Ra instead of his comrades so that they can flee, there are several extended cuts put in. Originally they were just ushered away by the natives, in the special edition they ride away on one of the Mastadges. Kurt Russell and James Spader are then seen lost in a sandstorm and found by the boys, and taken to the caves (which is in the theatrical edition); an additional scene after this sees the boys feeding the Mastadges outside the caves.