Amy Leversidge was elected unopposed following her nomination by Balpa’s national executive council (NEC).
She takes over from interim general secretary Miranda Rackley, who has stood in since Captain Martin Chalk retired earlier this year.
Leversidge will take up the post on 8 January whereby she will become the first woman to formally lead Balpa in its 86-year history.
She is currently assistant general secretary of the FDA union, which represents senior managers and professionals in public service.
Balpa executive president Paul Copland said: “Amy’s experience in her previous roles will add an extra dimension to our team and will help us continue to represent pilots and ensure action is taken on the issues that matter to our members.
"The new year will be a time of new challenges for Balpa, with a new NEC leadership and general secretary working together to ensure our members are at the heart of all we do."
Copland also paid tribute Rackley for her hard work and dedication in her interim role.
Leversidge said she was looking forward to "delivering real outcomes for pilots across the UK" and serving as a "strong and influential voice for the piloting profession".
"The airline industry contributes significantly to the UK economy and supports over a million jobs and pilots are at the heart of the industry. As the voice of UK pilots, Balpa will ensure our voice is influential with employers, regulators and government on the many challenges the airline industry faces."