Mark Dever offers the following helpful tips in his book, What Is a Healthy Church? (IX Marks; Wheaton: Crossway, 2007), p. 57:

Quick Tips: If You’re Thinking About Leaving a Church…

Before You Decide to Leave

  1. Pray.
  2. Let your current pastor know about your thinking before you move to another church or make your decision to relocate to another city. Ask for his counsel.
  3. Weigh your motives. Is your desire to leave because of sinful, personal conflict or disappointment? If it’s because of doctrinal reasons, are these doctrinal issues significant?
  4. Do everything within your power to reconcile any broken relationships.
  5. Be sure to consider all the “evidences of grace” you’ve seen in the church’s life—places where God’s work is evident. If you cannot see any evidences of God’s grace, you might want to examine your own heart once more (Matt. 7:3–5).
  6. Be humble. Recognize you don’t have all the facts and assess people and circumstances charitably (give them the benefit of the doubt).

If You Go

  1. Don’t divide the body.
  2. Take the utmost care not to sow discontent even among your closest friends. Remember, you don’t want anything to hinder their growth in grace in this church. Deny any desire to gossip (sometimes referred to as “venting” or “saying how you feel”).
  3. Pray for and bless the congregation and its leadership. Look for ways of doing this practically.
  4. If there has been hurt, then forgive—even as you have been forgiven.

Here are some additional very helpful thoughts from Tim Challies that he posted in an article titled When Should I Leave My Church?

Tim Challies lists the following reasons why you must leave a church.
If the teaching is heretical (Galatians 1:7-9).
If the leaders tolerate error from those who teach (Romans 16:17).
If there is utter disregard for biblical church discipline (1 Corinthians 5 and 2 Thessalonians 3:6,14).
If the church is marked by utter hypocrisy (2 Timothy 3:5).

He lists the following reasons why you may leave a church:
If you desire better teaching.
If you desire to use your gifts.
If you desire a more convenient location.
If it better serves your family.
Be sure to read the full article by clicking here.