Meaning: "Yes, something kind of similar to that, but not the exact same thing."
Note: this meaning can vary by degrees depending on the speaker.
This is a phrase I originally encountered in Thailand, although it seems prevalent in Cambodia, and Malaysia as well especially among taxi, tuk tuk, bus, and motorbike-taxi drivers and those that deal directly with foreigners such as myself.
Here's an example of the phrase as used in a real-life situation:
"Hmm, the 12:30 bus to Chiang Khong is full. Tell me, is there another bus leaving today?"
"And it goes to Chiang Khong?"
"Yes, same same, but different."
[in this case, "same same, but different" means that the bus has the same route but a different departure time]