Scintillation detectors were 3D printed based on a gamma knife (GK) dose distribution to calculate the volume averaging effect. The collimator output factors were measured using isodose-shaped scintillators (ISSs) and compared with those of a micro-diamond detector and previous reports. An absorbed dose distribution in a spherical dosimetry phantom with a radius of 8cm was obtained from GK treatment planning software (Leksell GammaPlan [LGP], Elekta AB, Stockholm, Sweden). Two types of ISSs were fabricated to fit the 97.2% (ISS-1) and 95.6% (ISS-2) isodose surfaces. The volume averaging correction factors were obtained by dividing the absorbed dose to water in the central voxel (CV) by that in the ISS. The correction effect due to the difference between the ISS and water was calculated by Monte Carlo simulations. Ten ISS detectors, five of each type, were used to measure the output factors of the 4- and 8-mm collimators of a GK Icon to assess system consistency. The output factors of seven GKs were measured using two ISS detectors, one of each type, and a PTW T60019 (PTW, Freiburg, Germany) micro-diamond detector. The detector output ratios (DORs) measured using the five ISSs of each type were consistent, with standard uncertainties less than 0.2%. In the 4-mm field, the volume averaging correction factor ratios were 1.018 and 1.026, and the output factors after all corrections were 0.827 (0.006) and 0.825 (0.006) for ISS-1 and ISS-2, respectively. In the 8-mm field, the volume averaging correction factor ratios were 1.000 for both ISS types, and the output factors were 0.898 (0.003) and 0.900 (0.003) for ISS-1 and ISS-2, respectively. The ISS detectors could measure the output factors of a GK with uncertainties comparable to that of the PTW 60019 detector. The output factors of all detectors decreased with the dose rate. The volume averaging effect of an ISS developed in-house could be calculated using known dose distributions. The collimator output factors of the GK Perfexion/Icon models measured using ISS detectors were consistent with those of a commercial synthetic micro-diamond detector and recent studies.