Rural Case Management Act of 1999 - Authorizes the Secretary of Health and Human Services to provide for an additional payment under title XVIII (Medicare) of the Social Security Act to rural service providers or physicians who furnish rural case manager services to Medicare beneficiaries.

Prohibits any payment for such case manager services furnished to a Medicare beneficiary unless the provider or physician establishes and periodically reviews a rural case management plan for the treatment of such beneficiary.

Requires the Secretary to establish the necessary standards for effective and efficient development and oversight of rural case manager services and management plans to: (1) ensure the health and safety of Medicare beneficiaries furnished plan services; and (2) provide guidance on the process or processes that may be used to timely develop such plans.

Provides that Medicare limitations on certain physician referrals shall apply to a referral by a rural case manager to a rural agency in the same manner as such limitations apply to a referral by a physician to an entity with which the physician has a financial relationship.