A new boundary element method (BEM) based method is described for the design of coils for magnetic resonance imaging (MRI) systems. BEM is an effective approach for solving the electromagnetic forward problem and has been used in the design of MRI gradient coils. However, BEM-based gradient coil design faces an ill-posed mathematical problem, which is conventionally handled by means of a Lagrange multiplication method. This work attempts to improve the BEM method for MRI coil designs by applying the Tikhonov regularization scheme to solve the ill-posed matrix system formulated by the BEM forward model. The objective of the study is not to design some specific gradient or radio-frequency (RF) coils for MRI system, but to discuss the design scheme with practical regularization and constraints. The proposed approach was explained in the design of MRI coils including biplanar transverse gradient coils and RF phased array coils. With the consideration of the practical engineering requirements, physical constraints such as wire intervals are transformed into mathematical constraints and formulated into BEM equations. The examples demonstrate that the proposed method is efficient and flexible for the design of MRI coils with arbitrary geometries and engineering constraints.