Introduction Application of organic fertilizer is a major approach to managing soil fertility and plant nutrition which can alleviate chemical contaminations, preserve soil biodiversity and the quantitative and qualitative yield of crops expected to be increased in sustainable agricultural systems. Consequently, demand for organic products has increased due to health and sustainable environment consideration, particularly for medicinal products. Intercropping is the cropping system of growing two or more crops simultaneously in the same field and is a sustainable method for increasing crop production compared with sole crop. The main objective of the study was to determine the effect of vermicompost and intercropping patterns on seed yield and macro and micronutrients uptake of fennel (Foeniculum vulgare Mill. ) and faba bean (Vicia faba L. ). Materials and Methods In order to compare the different intercropping patterns of fennel and faba bean under the application of vermicompost fertilizer, a field experiment was conducted as factorial based on a randomized complete block design with three replications at the Research Farm of the Faculty of Agriculture, University of Urmia, Iran, during the growing season of 2018. The first factor consisted of six cropping patterns including sole cropping of fennel and faba bean, one row of fennel+ one row of faba bean, two rows of fennel+ two rows of faba bean, three rows of faba bean+ two rows of fennel, four rows of faba bean+ two rows of fennel) and the second factor included the non-application and application of vermicompost (10 t ha-1). Plant samples were digested according to Jones and Case (1990) procedure. Seeds of faba bean and fennel were analyzed for macro-and micronutrients. In addition, Area Time Equivalent Ratio (ATER) was calculated to determine the advantages of intercropping. The analysis of variance was performed using SAS 9. 4 software. Means were compared using Duncan's test at the 5% probability level. Results and Discussion The results showed that the effect of cropping pattern on all measured traits was significant. The results revealed that the seed yield of fennel and faba bean increased following the application of vermicompost fertilizer. Moreover, concerning the effect of cropping patterns, the highest seed yield of fennel (2568. 33 kg. ha-1) and faba bean (2851. 67 kg. ha-1) were obtained in the sole cropping of these two plants. The higher production in fennel and faba bean sole cropping may be due to the less disturbance in the habitat in homogeneous environment under sole cropping systems. The highest amounts of N, P, K, Ca, Mg, Fe, Zn, Cu, and Mn were obtained in the treatments of intercropping and vermicompost application. The higher concentrations of nutrients in intercropping pattern could be explained by increasing root exudation and also better use of available resources that increased the accessibility of nutrients for component plants. The highest ATER (1. 14) was obtained in the three rows of faba bean+ two rows of fennel intercropping system fertilized with vermicompost. According to the ATER, it seems that three rows of faba bean+ two rows of fennel under the application of vermicompost was suitable for increasing productivity and making the best usage of environmental resources in order to achieve an optimal production, decrease costs and dependence on external inputs, and reducing pollution and environmental pressures on sustainable agricultural systems. Conclusions In general, the results of this experiment showed that the faba bean and fennel yield were influenced by different intercropping patterns and vermicompost. The highest seed yield for both plants (faba bean and fennel) were obtained in sole cropping. In the present study, the application of vermicompost could improve the yield of faba bean and fennel and nutrient uptake. It seems that the use of vermicompost in intercropping is one of the suitable strategies for achieving optimal yield with minimum inputs, which in the long term can reduce the need of chemical inputs for cropping systems.