How fast is Time running in Majora's Mask?

The only exception to the points Nolonar made is during the Last Six Hours - then, time flows at exactly 1 real world minute per in-game hour unless you've played the inverted song of time, in which case it flows at 3 real world minutes per in-game hour. Because of this, the actual conversion is as follows:

First Cycle: 27 seconds per hour until Midnight on the Third Day. 66 x 27 = 1782 seconds, or 29 minutes, 42 seconds until Midnight on the Third Day. Total time until moonfall: 35 minutes, 42 seconds

Second and subsequent Cycles: 45 seconds per hour until Midnight on the Third Day. 66 x 45 = 2970 seconds, or 49 minutes, 30 seconds until Midnight on the Third Day. Total time until moonfall: 55 minutes, 30 seconds.

Inverted Song of Time: 150 seconds per hour until Midnight on the Third Day. 66 x 150 = 9900 seconds, or 165 minutes, or 2 hours, 45 minutes until Midnight on the Third Day. Total time until moonfall: 3 hours, 3 minutes.

Old question, but there's some misinformation here I should clear up.

The in-game timer in Majora's Mask uses a 16-bit integer to represent one day. That means that over the course of one in-game day, it counts to 65536. Normally, it counts up by 3 per frame, and there are 20 frames in one second. This means that one in-game day lasts 65536/(3*20) = 1092.27 seconds (18:26.27). If the Song of Inverted Time is played, it counts up by 1 per frame, making each day last exactly three times longer, or 3276.8 seconds (54:36.8). At the start of the game, before you get the Ocarina of Time, time indeed moves faster--the timer counts up 5 per frame. This means the total time of a single in-game day is 40% less, or 655.36 seconds (10:55.36).

Contrary to Auro's answer, this does not change during the last 6 hours. What he may be thinking of is that when you go to confront Skull Kid, the in-game timer stops. Regardless of how much time was left, 5 real minutes will be put on the clock, then it's game over. Oddly, this is actually 24 seconds longer than the 6 in-game hours that it would have taken for the moon to fall on its own.

In summary,

• Normal length of one in-game day is 18:26.27. (total time 54:36.80, 45.51 seconds per hour)
• Slowed length of one in-game day is 54:36.80. (total time 2:43:50.40, 2:16.53 per hour)
• Length of one in-game day in the first cycle is 10:55.36. (total time 32:46.08, 27.31 seconds per hour)

Lastly, the in-game timer stops during all cutscenes, loading zones, and the start menu, as well as inside the clock tower and in boss rooms after the boss is defeated. So your actual play time will be longer than this over the course of an in-game day.

The Three Day Period lasts for 72 hours in-game, and it lasts about 54 minutes in our world. The Inverted Song of Time, however, can slow the time down just a pinch. Basically what everyone says simplified. One second in real life would be the equivalent of one minute is Majora's Mask. Time is also stopped when speaking or when in the clock tower basement.