Magnetic Resonance Imaging (MRI) is useful to provide detailed anatomical information such as images of tissues and organs within the body that are vital for quantitative image analysis. However, typically the MR images acquired lacks adequate resolution because of the constraints such as patients’ comfort and long sampling duration. Processing the low resolution MRI may lead to an incorrect diagnosis. Therefore, there is a need for super resolution techniques to obtain high resolution MRI images. Single image super resolution (SR) is one of the popular techniques to enhance image quality. Reconstruction based SR technique is a category of single image SR that can reconstruct the low resolution MRI images to high resolution images. Inspired by the advanced deep learning based SR techniques, in this paper we propose an autoencoder based MRI image super resolution technique that performs reconstruction of the high resolution MRI images from low resolution MRI images. Experimental results on synthetic and real brain MRI images show that our autoencoder based SR technique surpasses other state-of-the-art techniques in terms of peak signal-to-noise ratio (PSNR), structural similarity (SSIM), Information Fidelity Criterion (IFC), and computational time.