An improved apparatus for processing sea cucumbers having stages for orienting/aligning, cutting, splitting, flattening, eviscerating and cleaning the sea cucumber, and for collecting the eviscerated innards. A method for the automated splitting and evisceration of sea cucumbers using the apparatus of the present disclosure. A flattening plate and trough during the orienting/aligning step relax the sea cucumber and discourage its defence mechanisms. A wedge shaped flattening plate splits and flattens the sea cucumber immediately after the incision. Pronged discs maintain positioning of the sea cucumber during an aggressive wash and brush cleaning cycle, which may be repeated. Optionally, a vacuum may suction off a portion of the innards prior to cleaning.