Focused ultrasound is a promising therapeutic technique, as it involves the focusing of an ultrasonic beam with sufficient acoustic energy into a target brain region with high precision. Low-intensity ultrasound transmission by a single-element transducer is mostly established for neuromodulation applications and blood–brain barrier disruption for drug delivery. However, transducer positioning errors can occur without fine control over the sonication, which can affect repeatability and lead to reliability problems. The objective of this study was to determine whether the target brain region would be stable under small displacement (0.5 mm) of the transducer based on numerical simulations. Computed-tomography-derived three-dimensional models of a rat head were constructed to investigate the effects of transducer displacement in the caudate putamen (CP) and thalamus (TH). Using three different frequencies (1.1, 0.69, and 0.25 MHz), the transducer was displaced by 0.5 mm in each of the following six directions: superior, interior, anterior, posterior, left, and right. The maximum value of the intracranial pressure field was calculated, and the targeting errors were determined by the full-width-at-half-maximum (FWHM) overlap between the free water space (FWHMwater) and transcranial transmission (FWHMbase). When the transducer was positioned directly above the target region, a clear distinction between the target regions was observed, resulting in 88.3%, 81.5%, and 84.5% FWHMwater for the CP and 65.6%, 76.3%, and 64.4% FWHMwater for the TH at 1.1, 0.69, and 0.25 MHz, respectively. Small transducer displacements induced both enhancement and reduction of the peak pressure and targeting errors, compared with when the transducer was displaced in water. Small transducer displacement to the left resulted in the lowest stability, with 34.8% and 55.0% targeting accuracy (FWHMwater) at 1.1 and 0.69 MHz in the TH, respectively. In addition, the maximum pressure was reduced by up to 11% by the transducer displacement. This work provides the targeting errors induced by transducer displacements through a preclinical study and recommends that attention be paid to determining the initial sonication foci in the transverse plane in the cases of small animals.