Abstract Background Pain is usually subjective and thus it is challenging to describe its characteristics such as nature, intensity, and origin. Non-invasive methods such as assessing salivary alpha-amylase (SAA) may aid the practitioner to evaluate the pain intensity. Hence, the current study aimed to correlate the levels of SAA with the pain intensity in patients presenting with varied endodontic pain levels. Methods Sixty patients who presented with varied intensities of endodontic pain were selected for the present study out of which seven patients were excluded/dropped, leaving a total sample of fifty-five patients for assessment. Mandibular molar with symptomatic irreversible pulpitis without periapical pathology were included in the study. A 5ml of un-stimulated was obtained from the patients, following which the local anesthesia was administered. Root canal treatment was then performed and the pain scores at pre-operative and post-operative were recorded. Additionally, salivary samples were collected after emergency endodontic treatment and sent for sialochemical analysis. IBM.SPSS statistics software 23.0 was employed to assess the obtained data. Results A statistically significant drop in the pain score (P < 0.001) and SAA levels (P < 0.001) were observed post-operatively in the contract to pre-operative state. A strong positive correlation was reported between SAA levels and pain scores in patients undergoing emergency endodontic treatment at both time intervals namely pre-operative (P < 0.001) and post-operative (P < 0.001). Conclusion The results of this preliminary showed a strong association between the pain score and SAA levels in patients undergoing an emergency endodontic treatment.