Pregnancy is not a disqualifying condition under FAR Part 67. FAA recommends that pilots consult with their obstetrician about their flying activities and consult with their AME concerning flying during the third trimester in particular. Pertinent to all pilots is FAR § 61.53 which prohibits acting as PIC or in another required capacity with a known medical condition that would make them unable to meet the requirements for the medical certificate.
For pregnant pilots who fly for a living, the general starting point is that their employment is often at-will. However, there are exceptions under federal, state, and local discrimination and leave protection laws. At the federal level is Title VII of the Civil Rights Act (1964), which prohibits sex discrimination. In 1978 Congress passed the Pregnancy Discrimination Act to amend Title VII and prohibit sex discrimination based on pregnancy, childbirth, and related medical conditions. Often the size of the company is a factor for protection eligibility; however, pilots employed at any size company may find protections under the various human rights laws at the state and local levels.
Further protections in the form of accommodations or leave may be found in the Americans with Disabilities Act, Family and Medical Leave Act, and state and local laws. Pregnant pilots concerned with Employment Law matters should seek local legal counsel.