Background: Young refugees are at increased risk of labor market marginalization (LMM). We sought to examine whether the association of multimorbidity patterns and LMM differs in refugee youth compared to Swedish-born youth and identify the diagnostic groups driving this association. Methodology: We analyzed 249,245 individuals between 20–25 years, on 31 December 2011, from a combined Swedish registry. Refugees were matched 1:5 to Swedish-born youth. A multimorbidity score was computed from a network of disease co-occurrences in 2009–2011. LMM was defined as disability pension (DP) or >180 days of unemployment during 2012–2016. Relative risks (RR) of LMM were calculated for 114 diagnostic groups (2009–2011). The odds of LMM as a function of multimorbidity score were estimated using logistic regression. Results: 2841 (1.1%) individuals received DP and 16,323 (6.5%) experienced >180 annual days of unemployment during follow-up. Refugee youth had a marginally higher risk of DP (OR (95% CI): 1.59 (1.52, 1.67)) depending on their multimorbidity score compared to Swedish-born youth (OR (95% CI): 1.51 (1.48, 1.54)); no differences were found for unemployment (OR (95% CI): 1.15 (1.12, 1.17), 1.12 (1.10, 1.14), respectively). Diabetes mellitus and influenza/pneumonia elevated RR of DP in refugees (RRs (95% CI) 2.4 (1.02, 5.6) and 1.75 (0.88, 3.45), respectively); most diagnostic groups were associated with a higher risk for unemployment in refugees. Conclusion: Multimorbidity related similarly to LMM in refugees and Swedish-born youth, but different diagnoses drove these associations. Targeted prevention, screening, and early intervention strategies towards specific diagnoses may effectively reduce LMM in young adult refugees.