Nonprofit Mortgage Licensing Clarification Act of 2009 - Amends the S.A.F.E. Mortgage Licensing Act of 2008 to permit a state to exempt from certain registration or licensing requirements any charitable organization exempt from federal tax (including their employees and agents acting as loan originators), if the organization: (1) executes loan originations in order to promote or facilitate homeownership for certain low-income, disabled, or other disadvantaged persons or families; (2) offers loans at interest rates lower than the bank prime loan rate, or that are no-interest loans or loans with interest rates significantly below those for loans to purchase generally available single-family housing; and (3) does not otherwise engage in the business of a loan originator or mortgage broker.