Peace is replaced with a new goal, 'Monument', which focuses on player's efforts to establish the monuments needed within their city players will usually be given the knowledge of the monuments they need to build in the goals during a briefing of their next mission. Goals: While Population, Prosperity and Culture are still retained in the game, Favor is renamed as 'Kingdom' and maintains the same function in that the score is based upon the ruling Pharaoh's view on a player's performance to meeting their goals, bolstered by gifts sent to them.While many of the elements of the game, from housing to industry, borrows from Caesar III, the game distinguishes itself with some notable differences and some new features: Although the puzzle-like aspect of Pharaoh keeps the simulation far from realistic, the game stays true to the chronological order and timing of major events in the history of Egypt, including monument construction, wars and national disasters, the births and deaths of notable leaders, and the founding and fall of ancient cities.

While the game uses the deben as its currency, in reality it is not the case as no standardised pieces of metal have been found to indicate the actual currency of Ancient Egypt. All aspects of city life, such as housing, religion, warfare, and trade, are designed carefully to closely reflect that of actual Ancient Egyptian cities of the time, including the goods and services that they had available, with names of various pharaohs used in the game along with the appearance of historical characters from the period of Egypt's ancient history limited encyclopedic information about ancient Egyptian practices is provided in the game's help menu and instruction booklet. Much of the control is managed through the mouse and keyboard-shortcuts, with the game using an interface system like Caesar III, with buttons incorporated on it linked to different types of construction the player needs for their city (housing, roads, schools, warehouses, etc.), as well as buttons to view messages, undo mistakes and cycle through trouble-spots, along with a map of the region Ancient Egypt extended into, a group of advisers, called Overseers, that the player can rely on for information on the city's development and any problems encountered, and in-game overlays that can detail any rising issues and if housing is getting what it needs for its current level.

Pharaoh is played from a two dimensionalisometric perspective, with the magnification level fixed but the viewing angle able to be changed, but only at 90 degree angles, either counter-clockwise or clockwise.

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