Small Manufacturer Protection Act of 2013 - Amends the Federal Food, Drug, and Cosmetic Act to direct the Secretary of Health and Human Services (HHS) to grant the owner of a human generic drug facility a waiver from, or reduction of, one or more human generic drug fees if the Secretary finds that the assessment of the fee would present a significant barrier to market entry because of the owner's limited resources or other circumstances.

Requires an owner seeking such fee waiver or reduction to submit a written request no later than 180 days after the fee is due.

Prohibits the Secretary, in determining whether to grant such waiver or reduction, from considering anything other than the circumstances and assets of the owner and any affiliate of the owner.

Makes these provisions applicable to fees authorized to be assessed and collected for FY2014-FY2017.