Introduction Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting both upper and lower motor neurons, and lead to respiratory failure. Strategies are suggested to respiratory management in ALS patients, as the breath stacking and Expiratory muscle training (EMT), which have been used as aid to assist cough in neuromuscular disorders. However, the randomized controlled trials performed in ALS patients have not investigated the addiction of EMT together breath stacking in this population. This trial aims to determine if breath stacking plus EMT is more effective than breath stacking alone to decrease the decline rate on the inspiratory/expiratory muscle strength, FVC and voluntary PCF in ALS patients. Methods This parallel-group, assessor-blinded randomized controlled trial, powered for superiority, aims to assess pulmonary function, respiratory muscle strength, peak cough flow as primary outcomes. Forty-two participants are being recruited referral neuromuscular disease center at Brasilia, Brazil. Following baseline testing, participants are randomized using concealed allocation, to receive either: a) breath stacking technique alone or b) breath stacking technique plus EMT. Conclusion There is a lack of evidence regarding the benefit of EMT plus breath stacking in ALS patients. This trial will contribute to evidence currently being generated in national and international trials by implementing and evaluating a respiratory therapy program including two components not yet combined in previous research, for people with ALS involving longer-term follow-up of outcomes. This trial is ongoing and currently recruiting. Trial registration This trial was prospectively registered on the Clinical Trials Registry NCT04226144.