An SEP IRA is a simplified employee pension individual retirement account. It works as a type of IRA for people who are business owners and run groups with a minimal number of employees. An SEP IRA works like a standard type of IRA in that taxes are deferred and all contributions are deductible. A person can contribute twenty percent of one’s annual income if self-employed to a total of up to $49,000 a year. For employees, there is a limit of twenty-five percent per year.