In patients with thalassemia major (TM), cardiac magnetic resonance feature-tracking (CMR-FT) has been shown to be an effective method for diagnosing subclinical left ventricular (LV) dysfunction. This study aimed to determine whether CMR-FT could detect abnormal RV dysfunction in patients with a normal right ventricular ejection fraction (RVEF). We performed a retrospective analysis of TM patients admitted to Dubai’s Rashid Hospital between July 2019 and March 2021. The inclusion criteria were TM patients with SSFP cine with T2* (T2*-weighted imaging), while exclusion criteria included any other cardiovascular disease. When there was no myocardial iron overload (MIO) (T2* ≥ 20 ms) and when there was significant MIO (T2* < 20 ms), the CMR-FT was used to correlate with EF. Among the 89 participants, there were 46 men (51.7%) and 43 women (48.3%), with a mean age of 26.14 ± 7.4 years (range from 10 to 48 years). Forty-six patients (51.69%) did not have MIO, while 43 individuals did (48.31%). Thirty-nine patients (32.6%) were diagnosed with severe MIO, while seventeen (19.1%) were diagnosed with mild to moderate MIO. A significant correlation existed between RVEF and T2* values (r = 0.274, p = 0.014) and between left ventricular ejection fraction (LVEF) and T2* values (r = 0.256, p = 0.022). Using a multiple logistic regression model with predictors such as right ventricular longitudinal strain (RVGLS), LV ejection fraction (LV EF), and hemoglobin, abnormal myocardial iron overload can be predicted. This model demonstrates an AUC of 78.3%, a sensitivity of 72%, and a specificity of 76%. In the group with preserved RVEF > 53%, the left ventricular radial strain (LVGRS) (p = 0.001), right ventricular radial strain (RVGRS) (p = 0.000), and right ventricular basal circumferential strain (RVGCS-basal) (p = 0.000) CMR-FT strain values are significantly lower than those of the control group (p > 0.05). There was no significant correlation between the LVGLS and T2*. RVGLS was ranked among the most accurate predictors of abnormal myocardial iron overload. The LVGRS, RVGRS, and RVGCS-basal CMR-FT strain values were the best predictors of subclinical RV dysfunction in the group with preserved RVEF. The most accurate way to diagnose MIO is still T2*, but FT-strain can help us figure out how MIO affects the myocardium from a pathophysiological point of view.