The enzyme endo-inulinase hydrolyzes inulin to short chain fructooligosaccharides (FOS) that are potential prebiotics with many health promoting benefits. Although the raw materials for inulin production are inexpensive and readily available, commercial production of FOS from inulin is limited due to inadequate availability of the enzyme source. This study aimed to identify the fungi capable of producing endo-inulinase based on the in silico analysis of proteins retrieved from non-redundant protein sequence database. The endo-inulinase of Aspergillus ficuum was used as reference sequence. The amino acid sequences with >90% sequence coverage, belonging to different fungi were retrieved from the database and used for constructing three-dimensional (3D) protein models using SWISS-MODEL and Bagheerath H. The 3D models of comparable quality as that of the reference endo-inulinase were selected based on QMEAN Z score. The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular dynamic simulation analyses. A total of 230 proteins belonging to 53 fungal species exhibited sequence coverage >90%. Sixty one protein sequences with >60% sequence identity were modeled as endo-inulinase with higher QMEAN Z Score. The evaluations and validations of these 61 selected models for different structural and functional qualities revealed that 60 models belonging to 22 fungal species exhibited native like structure and unique motifs and residues as that of the reference endo-inulinase. Further, these models also exhibited similar kind of interaction between the active site around the conserved glutamate residue and substrate as that of the reference endo-inulinase. In conclusion, based on the current study, 22 fungal species could be identified as endo-inulinase producer. Nevertheless, further biological assessment of their capability for producing endo-inulinase is imminent if they are to be used for commercial endo-inulinase production for application in FOS industry.