Background The cultivation of empathy for healthcare providers is an important issue in medical education. Narrative medicine (NM) has been shown to foster empathy. To our knowledge, there has been no research that examines whether a NM programme affects multi-professional healthcare providers’ empathy. Our study aims to fill this gap by investigating whether a NM programme effects multi-professional healthcare providers’ empathy. Methods A pre-post questionnaire method was used.142 participants (n = 122 females) who attended the NM programme were divided into single (n = 58) and team groups (n = 84) on the basis of inter-professional education during a period of 2 months. Perceptions of the NM programme were collected using our developed questionnaire. Empathy levels were measured using the Chinese version of Jefferson Scale of Empathy - Healthcare Providers Version (JSE-HP) – at three time points: prior to (Time 1), immediately after (T2), and 1.5 years (T3) after the programme. Results Participants’ perceptions about the NM programme (n = 116; n = 96 females) suggested an in enhancement of empathy (90.5%). Empathy scores via the JSE-HP increased after the NM programme (T1 mean 111.05, T2 mean 116.19) and were sustainable for 1.5 years (T3 mean 116.04) for all participants (F(2297) = 3.74, p < .025). A main effect of gender on empathy scores was found (F(1298) = 5.33, p < .022). No significant effect of gender over time was found but there was a trend that showed females increasing empathy scores at T2, sustaining at T3, but males demonstrating a slow rise in empathy scores over time. Conclusions NM programme as an educational tool for empathy is feasible. However, further research is needed to examine gender difference as it might be that males and females respond differently to a NM programme intervention. Electronic supplementary material The online version of this article (doi:10.1186/s12909-017-0952-x) contains supplementary material, which is available to authorized users.