Recent reports show that focusing attention on the location where pain is expected can enhance its perception. Moreover, crossing the hands over the body’s midline is known to impair the ability to localise stimuli and decrease tactile and pain sensations in healthy participants. The present study investigated the role of transient spatial attention on the perception of painful and non-painful electrical stimuli in conditions in which a match or a mismatch was induced between skin-based and external frames of reference (uncrossed and crossed hands positions, respectively). We measured the subjective experience (Numerical Rating Scale scores) and the electrophysiological response elicited by brief electric stimuli by analysing the P3 component of Event-Related Potentials (ERPs). Twenty-two participants underwent eight painful and eight non-painful stimulus blocks. The electrical stimuli were applied to either the left or the right hand, held in either a crossed or uncrossed position. Each stimulus was preceded by a direction cue (leftward or rightward arrow). In 80% of the trials, the arrow correctly pointed to the spatial regions where the stimulus would appear (congruent cueing). Our results indicated that congruent cues resulted in increased pain NRS scores compared to incongruent ones. For non-painful stimuli such an effect was observed only in the uncrossed hands position. For both non-painful and painful stimuli the P3 peak amplitudes were higher and occurred later for incongruently cued stimuli compared to congruent ones. However, we found that crossing the hands substantially reduced the cueing effect of the P3 peak amplitudes elicited by painful stimuli. Taken together, our results showed a strong influence of transient attention manipulations on the NRS ratings and on the brain activity. Our results also suggest that hand position may modulate the strength of the cueing effect, although differences between painful and non-painful stimuli exist.