Manufacturing Innovation in America Act of 2013 - Amends the Internal Revenue Code to allow a taxpayer to elect a tax deduction for an amount equal to 71% of the lesser of: (1) the taxpayer's patent box profit, or (2 the taxpayer's taxable income for the taxable year. Defines "patent box profit" to include gross receipts derived from the sale, lease, license, or or other disposition of qualified patent property in the course of a U.S. trade or business over the sum of the taxpayer's cost of goods sold allocable to patent gross receipts, other expenses, losses, or deductions, including research and development expenditures, allocable to such receipts, plus routine profit. Defines "qualified patent" to include a patent issued or extended by, or for which an application is pending before, the United States Patent and Trademark Office (USPTO).

Sets forth rules for the application of the patent box profit deduction to pass-thru entities, including partnerships and S corporations, trusts and estates, and agricultural and horticultural cooperatives.