Multiple factors contribute to symptom generation and treatment response in proton-pump inhibitor non-responders (PPI-NRs). We aimed to test whether PPI-NRs with normal acid exposure have a higher degree of esophageal hypersensitivity and hypervigilance and can be identified using functional lumen imaging probe (FLIP) topography at the time of endoscopy. Data from PPI-NRs whom underwent endoscopy, FLIP and wireless 96-h pH-metry were retrospectively analyzed. Patients were grouped according to acid exposure time (AET) as (a) 0days abnormal (AET > 6%), (b) 1-2days abnormal, or (c) 3-4days abnormal. The esophageal hypervigilance and anxiety scale (EHAS) score and other symptom scores were compared between groups. The discriminatory ability of the esophagogastric junction (EGJ) distensibility index (DI) and max EGJ diameter in identifying patients with 0days abnormal AET was tested via receiver-operating-characteristic (ROC) curve analysis. EHAS score was 38.6 in the 0days abnormal AET group, 30.4 in the 1-2days abnormal AET group (p = 0.073 when compared to 0days abnormal) and 28.2 in the 3-4days abnormal AET group (p = 0.031 when compared to 0days abnormal). Area-under-the-curve (AUC) for the DI in association with 0days AET > 6% was 0.629. A DI of < 2.8 mm2/mmHg had a sensitivity of 83.3%, and negative predictive value of 88% in classifying patients with 0days abnormal acid exposure (p = 0.004). FLIP complements prolonged wireless pH-metry in distinguishing the subset of PPI-NRs with completely normal acid exposure and a higher burden of esophageal hypervigilance. Proper identification of patients along the functional heartburn spectrum can improve overall surgical outcomes.