In this study, we investigated whether the Achilles tendon reflex (ATR) in healthy infants is modulated by changes in body position (prone vs. supine). The amplitude of the ATR was compared at postnatal day 1, months 2, 3 and 6, while infants were placed in prone and supine position. The ATR was considered “positive” when at least 1 of 20 tendon taps evoked a visible contraction of the ankle plantar flexor muscles. At 6 months, the amplitude and latency of the ATR were evaluated by electromyographic (EMG) recordings of the (lateral and medial) gastrocnemius muscle, with the infant in prone and supine position. At postnatal day 1, the clinical ATR response was more frequently present in prone than supine position (14/16 or 88% vs. 4/16 or 25%, respectively, p < 0.01). From 2 months onwards, the frequencies of positive ATRs were no longer significantly different between prone (14/14 or 100%) and supine position (10/14 or 67%). However, based on the EMG recordings at 6 months, the ATR amplitude was higher in prone compared to supine position ( n = 8, median 5.5 mV, range 4.7–6.6 mV; and median 3.8 mV, range 2.3–5.6 mV, p < 0.05). We conclude that the ATR response in healthy infants is more pronounced in prone than in supine position, either when clinically (visually) assessed during routine tendon tapping or when neurophysiologically assessed during surface EMG recording.