In Big Pharma the player takes the role of manager of a pharmaceutical company, producing medications from raw materials.

This is done in an isometric perspective depicting a floorplan with various ports along the edges that can be used to bring in materials or ship out completed drugs.

The player can click on processes or materials to evaluate their current state, thus giving them the ability to debug the production line.

Once the player has produced a complete pill from specific materials for the first time and delivered it to an output port, they are given the opportunity to name the product.

Scenarios in the game include competing companies that will also be releasing prescription drugs that will impact the profitability of the player's products.