Background Presumably bundling/co-packaging of zinc with ORS encourages the combined use of the products for diarrhea treatment; however, empirical evidences are scarce. The purpose of this work is to evaluate whether co-packing using a plastic pouch can enhance the joint adherence to the treatment or not. The study also compares the cost effectiveness (CE) of two co-packaging options: ‘central’ and ‘health center (HC)’ level bundling. Methods This cluster-randomised controlled trial was conducted in 2015 in eight districts of Ethiopia. Thirty two HCs were randomly assigned to one of the following four intervention arms: (i) ‘Central bundling’ (zinc and ORS bundled using a pouch that had instructional message, distributed to HCs); (ii) ‘HC level bundling’ (zinc, ORS and a similar pouch distributed to the HCs and bundled by health workers); (iii) ‘Bundling without message’ (zinc, ORS and plain pouch distributed and bundled by the health workers); and, (iv) ‘Status quo’ (zinc and ORS co-administered without bundling). In each of the four arms, 176 children 6–59 months of age, presented with acute diarrhea were enrolled. Twelve days after enrollment, level of adherence was assessed. A composite scale of adherence was developed and modeled using mixed effects linear regression analysis. The unit costs associated with the arms were estimated using secondary data sources. Incremental CE analysis was made by taking the cost and level of adherence in fourth arm as a base value. Results The follow-up rate was 95.6 %. As compared with the ‘status quo’ arm, the joint adherences in the ‘central’ and ‘HC level’ bundling arms raised substantially by 14.8 and 15.7 percentage points (PP), respectively (P < 0.05). No significant difference was observed between ‘bundling without message’ and the ‘status quo’ arms. The unit cost incurred by the ‘central bundling’ is relatively higher (USD 0.658/episode) as compared with the ‘HC level bundling’ approach (USD 0.608/episode). The incremental CE ratio in the ‘central bundling’ modality was two times higher than in the ‘HC based bundling’ approach. Conclusion Bundling zinc with ORS using a pouch with instructional messages increases adherence to the treatment. ‘HC level bundling’ is more CE than the ‘central bundling’ approach. Electronic supplementary material The online version of this article (doi:10.1186/s12889-016-3126-6) contains supplementary material, which is available to authorized users.