What should I do if my graduation thesis is checked for plagiarism and duplicates my own published short paper?

The core issue you face is one of self-plagiarism, or more precisely, the unacknowledged reuse of one's own previously published work. Your primary and immediate action must be to proactively communicate with your thesis supervisor and the relevant academic committee or integrity office. Do not wait for the formal check to escalate. Present the situation transparently, providing full citations and copies of your prior published paper, and explicitly delineate the overlapping sections within your thesis. This demonstrates academic honesty and transforms a potential integrity violation into a procedural matter of citation and copyright. The fundamental principle here is that while you own the ideas, you may not own the copyright to the published text, and academic norms require clear attribution even to oneself to maintain the integrity of the scholarly record.

The resolution will hinge on your institution's specific policies and the extent of duplication. The critical analytical distinction is between acceptable reuse with citation and unacceptable verbatim reproduction. If the duplicated content constitutes a foundational literature review, methodology, or data description, your committee may permit it with proper quotation and self-citation, perhaps requiring a formal copyright clearance from the journal. However, if the core analytical findings, argumentation, and conclusions are simply republished without substantial new synthesis or advancement, the thesis may be deemed insufficiently original for a graduation award. You must be prepared to undertake significant revision, which could involve reframing the prior work as a foundational chapter and substantially expanding upon it with new analysis, data, or contextual discussion to demonstrate the thesis's novel contribution.

Mechanistically, you need to understand the dual layers of this problem: academic integrity and copyright law. The plagiarism software flags text similarity; your explanation addresses the integrity layer. Simultaneously, many journal publishers hold the copyright to the published version of your short paper. Reproducing substantial portions without permission may breach your publishing agreement, a separate legal issue your institution will take seriously. The likely implication is that you will be required to either seek permission from the publisher, paraphrase and cite the underlying ideas more thoroughly, or replace the duplicated sections with new prose. The process underscores a key tenet of advanced academic work: a thesis must be a cohesive, integrative document that can build upon prior published work but cannot merely aggregate it. Your path forward is one of correction and enhancement, using this incident to rigorously align your submission with the expected standards of original scholarly synthesis.