Within the NaCo-ISPY exoplanet imaging program, we aim at detecting and characterizing the population of low-mass companions at wide separations ($gtrsim$10AU), focusing in particular on young stars either hosting a known protoplanetary disk or a debris disk. R CrA is one of the youngest (1-3 Myr) and most promising objects in our sample because of two previous studies that suggested the presence of a close companion. Our aim is to directly image and characterize the companion for the first time. We observed R CrA twice with the NaCo instrument at VLT in the $L$ filter with a one year time baseline in between. The high-contrast imaging data were reduced and analyzed, and in both datasets the companion candidate was detected. The companion is detected at a separation of $196.8pm4.5$/$196.6pm5.9$ mas ($18.7pm1.3$/$18.7pm1.4$ AU) and position angle of $134.7pm0.5^circ/133.7pm0.7^circ$ in the first/second epoch observation. We measure a contrast of $7.29pm0.18$/$6.70pm0.15$ mag with respect to the primary. Stellar proper motion study rejects the hypothesis of the signal being a background object. The companion candidate orbits in the clockwise direction and, if on a face-on circular orbit, its period is $sim43-47$ yr. This value disagrees with the estimated orbital motion and therefore a face-on circular orbit may be excluded. Depending on the assumed age, extinction and brightness of the primary, the stellar companion has a mass between $0.10pm0.02, M_odot$ and $1.03^{+0.20}_{-0.18},M_odot$ range, if no contribution from circumsecondary material is taken into account. The presence of the companion needs to be taken into account when analyzing the complex circumstellar environment of R CrA.