After graduating from Iowa, Fernandes worked for Northeastern University before coming to Gallaudet as chair of Sign Communication. Her next move was to Hawaii where she established an Interpreter Training Program and served for five years as the director of the Hawaii School for the Deaf and the Blind. On April 15, 2014, Fernandes was named the 9th President of Guilford College. She succeeded Kent Chabotar on July 1, 2014, becoming the first woman to hold this position. On August 26, 2015, Fernandes was formally inaugurated as the first female and the ninth president of Guilford College.
In 1995 Fernandes returned to Gallaudet to become the vice president for the Laurent Clerc National Deaf Education Center. In 2000, she was named provost of the university by President I. King Jordan, who appointed her without consulting the faculty, a move which Jordan called "a terrible mistake". In her application for the university presidency Fernandes wrote: Immediately after the announcement of the appointment of Fernandes as Gallaudet University president, scores of students protested against her appointment. According to The Washington Post, "Students objected to the appointment of Jane Fernandes, who is deaf and is currently the university's provost, because she did not grow up using American Sign Language. Some students also criticized Fernandes for not having warm relations with students." Opponents of Fernandes claim that the Washington Post article, were unable to figure out the real reasons for their opposition, although a frequently published reason was that she was "not Deaf enough." The protesters pointed to her past managerial actions that they felt were questionable and did not reflect qualities of a solid leader. Fernandes also attracted opposition due to a perception that she was insufficiently committed to addressing the problem of audism. The student paper took polls a few days before the selection. Of those faculty members who responded, 36% gave Fernandes an "acceptable" rating, compared to 53% and 64% for the two other finalists. On October 29, 2006, the Board of Trustees of Gallaudet University rescinded her contract to be the ninth President of Gallaudet and terminated her in her position as President-designate.