There are growing concerns on stress among nurses in low- and middle-income countries (LMICs) in South-East Asia. It is important to improve mental health among nurses in these countries. The objective of this study was to examine the efficacy of two types of newly developed smartphone-based stress management programs in improving depressive and anxiety symptoms among hospital nurses in Vietnam. This study was a three-arm (including two intervention groups and one control group) randomized trial. Participants were recruited from nurses in a large general hospital in Hanoi, Vietnam. Two types (free-choice and fixed sequential order) of smartphone-based stress management programs were developed. Participants were randomly allocated to Program A (a free-choice, multimodule stress management), Program B (a fixed-order, internet cognitive behavioral therapy, iCBT), or a control group (treatment as usual). The depressive and anxiety symptoms were measured by using the Depression Anxiety and Stress Scales at baseline, 3-, and 7-month follow-up surveys. 951 participants were randomly allocated to each of the three groups. Program B showed a statistically significant effect on improving depressive symptoms at 3-month (p = 0.048), but not at 7-month (p = 0.92); Cohen’s d was − 0.18 (95% CI − 0.34 to − 0.02) and 0.03 (95% CI − 1.00 to 1.05), respectively. Program A failed to show a significant intervention effect on any of the outcomes at 3- or 7-month follow-up (p > 0.05). Despite the small effect size, the present fixed-order iCBT program seems effective in improving depression of hospital nurses in Vietnam. A public health impact of the intervention can be scalable, when considering its accessibility and minimal cost. Trial registration number: The study protocol is registered at the UMIN Clinical Trials Registry (UMINCTR; ID = UMIN000033139). Registered date of the protocol is 1st Jul. 2018. https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000037796