The progression of chronic kidney disease (CKD) can be directly or indirectly accelerated by a poor diet and the diet’s influence on risk factors for this disease. There have been no food frequency questionnaires (FFQs) developed for the assessment of diet in patients with CKD in Taiwan. This study analyzed the validity of a short FFQ (SFFQ) with 42 items for estimating patient intake of macronutrients, fiber, phosphorus, potassium, and calcium against 3-day dietary records (3-day DRs) in Taiwanese patients with stages 3–5 CKD. In an interview, 107 participants with the help of a dietician filled out an SFFQ and reviewed a 3-day DR the patients had filled out prior to the interview. Partial Pearson correlation coefficients between SFFQ and 3-day DR were 0.722, 0.619, 0.593, 0.572, 0.450, 0.611 and 0.410 for protein, fat, carbohydrate, fiber, phosphorus, potassium, and calcium, respectively, after adjusting for energy intake. Cross-classification analysis revealed 63.5–83.2% similarity in cross-tool estimated intakes of macronutrients, fiber, phosphorus, potassium, and calcium in the same quartiles or adjacent ones. Bland–Altman plots revealed good agreement between the two tools along different intake levels. In conclusion, the newly developed SFFQ had moderate relative validity in estimating the usual intake of key nutrients related to nutrition management of patients with late-stage CKD, suggesting it can be used to assess dietary intakes in a population with CKD, especially in those residing in an Asian region.