Context : The Fornax Deep Survey ( FDS ) , an imaging survey in the u ’ , g ’ , r ’ , and i ’ -bands , has a supreme resolution and image depth compared to the previous spatially complete Fornax Cluster Catalog ( FCC ) . Our new data allows us to study the galaxies down to r ’ -band magnitude m _ { r ^ { \prime } } \approx 21 mag ( M _ { r ^ { \prime } } \approx -10.5 mag ) , which opens a new parameter regime to investigate the evolution of dwarf galaxies in the cluster environment . After the Virgo cluster , Fornax is the second nearest galaxy cluster to us , and with its different mass and evolutionary state , it provides a valuable comparison that makes it possible to understand the various evolutionary effects on galaxies and galaxy clusters . These data provide an important legacy dataset to study the Fornax cluster . Aims : We aim to present the Fornax Deep Survey ( FDS ) dwarf galaxy catalog , focusing on explaining the data reduction and calibrations , assessing the quality of the data , and describing the methods used for defining the cluster memberships and first order morphological classifications for the catalog objects . We also describe the main scientific questions that will be addressed based on the catalog . This catalog will also be invaluable for future follow-up studies of the Fornax cluster dwarf galaxies . Methods : As a first step we used the SExtractor fine-tuned for dwarf galaxy detection , to find galaxies from the FDS data , covering a 26 deg ^ { 2 } area of the main cluster up to its virial radius , and the area around the Fornax A substructure . We made 2D-decompositions of the identified galaxies using GALFIT , measure the aperture colors , and the basic morphological parameters like concentration and residual flux fraction . We used color-magnitude , luminosity-radius and luminosity-concentration relations to separate the cluster galaxies from the background galaxies . We then divided the cluster galaxies into early- and late-type galaxies according to their morphology and gave first order morphological classifications using a combination of visual and parametric classifications . Results : Our final catalog includes 14,095 galaxies . We classify 590 galaxies as being likely Fornax cluster galaxies , of which 564 are dwarfs ( M _ { r ^ { \prime } } ¿ -18.5 mag ) consisting our Fornax dwarf catalog . Of the cluster dwarfs we classify 470 as early-types , and 94 as late-type galaxies . Our final catalog reaches its 50 % completeness limit at magnitude M _ { r ^ { \prime } } = -10.5 mag and surface brightness \bar { \mu } _ { e,r ^ { \prime } } = 26 mag arcsec ^ { -2 } , which is approximately three magnitudes deeper than the FCC . Based on previous works and comparison with a spectroscopically confirmed subsample , we estimate that our final Fornax dwarf galaxy catalog has \lesssim 10 % contamination from the background objects . Conclusions :